Cbcb - User contributions [en]

Cbcb:Pop-Lab:How do I run the new Bambus

2009-10-31T21:19:42Z

Sergek:

The new Bambus (aka Bambus 2) actually consists of fourexecutables that run in order using a supplied AMOS bank. An important note, Bambus 2 is still an early beta. As such, it is advisable to back up
the bnk directory before using. Program documentation is also available on the command line by typing <command> -h.

The first program is clk. This program finds all mated reads within contigs and converts the mate distances to be relative to contigs rather than reads. The second program is Bundler. Bundler joins together
the contig link messages generated by clk together when they can be to create consensus links between contigs. It will output multiple contig links for a pair of contigs. The third program is MarkRepeats. This program identifies repeats using two methods, the first is shortest paths and the second is by examining a-stat on a component by component basis. The final program is OrientContigs.
OrientContigs uses the contig links to orient and order the contigs into scaffolds, as well as performing some simplification by joining contigs. Each of the programs is covered in more detail below. To get more
help on running any program use -h.

1. clk
- Modifies the bank to create contig edges. 
- Example: clk -b[ank] data.bnk

2. Bundler
- Bundle together contig edges to create contig links. 
- Example: Bundler -b[ank] data.bnk [-t[ype] comma separated list of edge types]
- The -t[ype] option allows only certain contig edges to be processed. ALL means use any type. The types are defined in src/AMOS/Link_AMOS.hh

3. MarkRepeats
- Run shortest paths and connected component repeat detection algorithms. This requires AMOS to be built with the Boost graph library available to it. 
- Example: MarkRepeats -b[and] data.bnk [-redundancy X -aggressive]
- The -redundancy ignores linka containing fewer than X edges.
- The -aggressive option marks contigs as repetitive based on global astat calculation rather than a connected component one.

4. OrientContigs
- Orient and order the contigs based on the links. This program uses a greedy algorithm to orient and order contigs relative to an arbitrary start contig. Edges that contradict the current scaffold are marked bad
and ignored for the rest of the analysis. They are still output but don't affect any subsequent calculations.

The output includes a a dot-formatted file, NCBI AGP scaffold formatted file, and xml files formatted to be compatible with Bambus 1 tools.

Note that this program does not currently linearize the scaffold but maintains them as a graph. This program also recursively simplifies common patters in the graph. Currently the patterns are
bubbles or straight lines. For example, contigs A->B->C will be simplified to just A. Also A->B->D will become A as well. This simplification is performed recursively until the graph is stable. Note that the
\>C/>
simplification updates the bank in a destructive way by removing contigs and replacing them (as well as their edges) with updated contigs.
The marking of the edges as BAD or GOOD also destructively updates the bank. Therefore it is necessary to make a backup of the bank before running this program. 
- Example: OrientContigs -b[ank] <bank_name> -prefix asm [-all -noreduce -redundancy X -repeats Y -aggressive].
- The - prefix option specifies the prefix to use for all output files.
- The -all option specifies whether disconnected contigs should be output as their own scaffolds or if they should be skipped.
- The -noreduce option turns off the graph simplification described above.
- The -redundancy option ignores links containing fewer than X edges.
- The -repeats option reads a file of repeats (Y) which specify one contig ID per line. Repeat contigs and their links are not used for odering/orienting any other data in the graph. Repeats are currently not resolved and are output as single-contig scaffolds. If known, these may be specified or the repeats identified by MarkRepeats (above) may be used.
- The -aggressive option will not mark edges that move a contig more than 3 STDEVS away as bad and will try to reconcile the positions.

Cbcb:Pop-Lab:How do I run the new Bambus

2009-10-31T21:19:17Z

Sergek:

The new Bambus (aka Bambus 2) actually consists of fourexecutables that run in order using a supplied AMOS bank. An important note, Bambus 2 is still an early beta. As such, it is advisable to back up
the bnk directory before using. Program documentation is also available on the command line by typing <command> -h.

The first program is clk. This program finds all mated reads within contigs and converts the mate distances to be relative to contigs rather than reads. The second program is Bundler. Bundler joins together
the contig link messages generated by clk together when they can be to create consensus links between contigs. It will output multiple contig links for a pair of contigs. The third program is MarkRepeats. This program identifies repeats using two methods, the first is shortest paths and the second is by examining a-stat on a component by component basis. The final program is OrientContigs.
OrientContigs uses the contig links to orient and order the contigs into scaffolds, as well as performing some simplification by joining contigs. Each of the programs is covered in more detail below. To get more
help on running any program use -h.

# clk
- Modifies the bank to create contig edges. 
- Example: clk -b[ank] data.bnk

# Bundler
- Bundle together contig edges to create contig links. 
- Example: Bundler -b[ank] data.bnk [-t[ype] comma separated list of edge types]
- The -t[ype] option allows only certain contig edges to be processed. ALL means use any type. The types are defined in src/AMOS/Link_AMOS.hh

3. MarkRepeats
- Run shortest paths and connected component repeat detection algorithms. This requires AMOS to be built with the Boost graph library available to it. 
- Example: MarkRepeats -b[and] data.bnk [-redundancy X -aggressive]
- The -redundancy ignores linka containing fewer than X edges.
- The -aggressive option marks contigs as repetitive based on global astat calculation rather than a connected component one.

4. OrientContigs
- Orient and order the contigs based on the links. This program uses a greedy algorithm to orient and order contigs relative to an arbitrary start contig. Edges that contradict the current scaffold are marked bad
and ignored for the rest of the analysis. They are still output but don't affect any subsequent calculations.

The output includes a a dot-formatted file, NCBI AGP scaffold formatted file, and xml files formatted to be compatible with Bambus 1 tools.

Note that this program does not currently linearize the scaffold but maintains them as a graph. This program also recursively simplifies common patters in the graph. Currently the patterns are
bubbles or straight lines. For example, contigs A->B->C will be simplified to just A. Also A->B->D will become A as well. This simplification is performed recursively until the graph is stable. Note that the
\>C/>
simplification updates the bank in a destructive way by removing contigs and replacing them (as well as their edges) with updated contigs.
The marking of the edges as BAD or GOOD also destructively updates the bank. Therefore it is necessary to make a backup of the bank before running this program. 
- Example: OrientContigs -b[ank] <bank_name> -prefix asm [-all -noreduce -redundancy X -repeats Y -aggressive].
- The - prefix option specifies the prefix to use for all output files.
- The -all option specifies whether disconnected contigs should be output as their own scaffolds or if they should be skipped.
- The -noreduce option turns off the graph simplification described above.
- The -redundancy option ignores links containing fewer than X edges.
- The -repeats option reads a file of repeats (Y) which specify one contig ID per line. Repeat contigs and their links are not used for odering/orienting any other data in the graph. Repeats are currently not resolved and are output as single-contig scaffolds. If known, these may be specified or the repeats identified by MarkRepeats (above) may be used.
- The -aggressive option will not mark edges that move a contig more than 3 STDEVS away as bad and will try to reconcile the positions.

Cbcb:Pop-Lab:Serge-Report

2009-02-12T23:50:22Z

Sergek:

= February =
February 16th, 2009: 
* I have been working on the materials for my preliminary exam. My preliminary paper is is available [[Media:PaperList.pdf|here]] and the preliminary paper is [[Media:Paper.pdf|here]].
* I have also met with Dr. Alan Sussman, a member of my preliminary committee, to discuss parallel option for graph algorithms. He pointed me to several papers on graph and hyper-graph partitioning. I had been thinking of doing randomized graph algorithms for speedup but using efficient partitioning, the standard graph algorithms can be distributed while minimizing communication. The other option is to use shared-memory machines which are more expensive and less available than distributed memory machines.
* I also implemented two methods for repeat detection in Bambus 2.
** The first splits the graph into strongly connected components using the SeqAn library. The astat is computed on each connected component separately. The motivation is to subdivide metagenomic samples into their constituent organisms and compute astat only on one organism at a time to avoid inadvertently marking abundant organisms as repeats
** The second computes all-to-all shortest paths and the number of shortest paths each node is on. The nodes that are on a large number of shortest paths (more than 1.5 stdev from mean) are marked as repetitive.
** Using the combination of these two approaches Brucella_suis_1330 correctly identifies repeats that were previously causing mis-assembly. I also tried the methods on Acid Mine but SeqAn was crashing.
* My next steps are to continue writing the preliminary paper, focusing on the proposed work section. I also plan to look at the results on Brucella_suis_1330 in detail to evaluate correctness of contig placement given my repeat identification.

File:Paper.pdf

2009-02-12T23:21:12Z

Sergek:

File:PaperList.pdf

2009-02-12T23:20:56Z

Sergek:

Cbcb:Pop-Lab:Serge-Report

2009-02-12T23:11:57Z

Sergek:

----
February 16th, 2009

Cbcb:Pop-Lab

2009-02-12T23:10:17Z

Sergek:

= Important pages =
* Group members [[Cbcb:Pop-Lab:Members]]
* Blog: [http://genomes.blogspot.com Genomes.blogspot.com]
* How-tos: [[Cbcb:Pop-Lab:How-to]] - List of documentation on how to perform certain analyses, use different software, etc.
* Software developed by us: [[Cbcb:Pop-Lab:Software]]

= Meetings/seminars =
* [[Pop_group_meeting|Group meeting]]: every Monday from 2:30pm in corner conference room (3120 C)
* [[seminars|CBCB seminar]]: Thursdays 2-3pm during the semester in main conference room

= Progress Reports =
* [[Cbcb:Pop-Lab:Niranjan-Report|Niranjan]]
* [[Cbcb:Pop-Lab:Chris-Report|Chris]]
* [[Cbcb:Pop-Lab:James-Report|James]]
* [[Cbcb:Pop-Lab:Serge-Report|Serge]]

= Pop Lab Presentations =
* [[Media:Xoo_Cripsr.odg|Xanthomonas Crispr Slides (openoffice format)]]
* Listeria Monocytogenes Slides (powerpoint)
* Metagenome pipelines overview [[Media:Pipeline_outline.pdf|Presentation(pdf)]]

Pop group meeting

2008-11-17T19:58:47Z

Sergek: /* 11/17/2008 */

= 09/29/2008 =

# Benjamin Langmead [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003263 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression] (PLoS one)
# Bo Liu [http://genomebiology.com/2008/9/9/R139 Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues] (Genome Biology)
# Daniela Puiu [http://genome.cshlp.org/cgi/reprint/gr.080200.108v1 Sequencing of natural strains of Arabidopsis thaliana with short reads] (Genome Research)
# Dan Sommer, Niranjan Nagarajan [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)
# James Robert White [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V73-4SHVST0-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=961305&md5=4115e7b8186a36db60f6b11a217a8798 Microbial population dynamics during aerobic sludge granulation at different organic loading rates] (ScienceDirect)
# Mohammad Reza Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/16/5180 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library] (NAR)
# Sergey Koren [http://www.biomedcentral.com/1471-2105/9/390 R/parallel - speeding up bioinformatics analysis with R] (BMC Bioinformatics)
# Theodore Gibbons [http://www.ncbi.nlm.nih.gov/pubmed/18711340 High-resolution metagenomics targets specific functional types in complex microbial communities] (Nature Biotechnology) [http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function] (Systems Microbiology)

= 10/06/2008 =
# Bo Liu [http://www.pnas.org/content/105/39/15076.short The convergence of carbohydrate active gene repertoires in human gut microbes.] PNAS
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/20/2395 SeqMap: mapping massive amount of oligonucleotides to the genome] Bioinformatics
# James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS
# MohammadReza Ghodsi [http://aem.asm.org/cgi/content/abstract/74/5/1453 Metagenomics: Read Length Matters] Applied Environmental Microbiology
# Sergey Koren [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads] PLoS Computational Biology

= 10/13/2008 =
# Daniela Puiu, Daniel Sommer [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003373 MetaSim—A Sequencing Simulator for Genomics and Metagenomics] PLoS ONE
# Bo Liu, James Robert White [http://www.sciencemag.org/cgi/content/full/322/5899/275 Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth.] Science
# MohammadReza Ghodsi [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2557142 Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets] (PLoS one)

MetaSim software:
Location: /fs/sz-user-supported/common/packages/MetaSim/
Executable(Java): /fs/sz-user-supported/common/packages/MetaSim/metasim/MetaSim
Database: /fs/sz-user-supported/common/packages/MetaSim/database
create a symlink to it from your working directory, otherwise you have to import it
NCBI databases: [ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz Complete bacteria]; [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz Taxonomy]

= 10/20/2008 =
# Bo Liu [http://www.pnas.org/content/105/37/13977.short?rss=1 Accelerated evolution of resistance in multidrug environments] PNAS [http://www.pnas.org/content/105/39/14918.short?rss=1 Drug interactions modulate the potential for evolution of resistance] PNAS
# Daniel Sommer [http://www.ncbi.nlm.nih.gov/pubmed/18927115?dopt=Abstract NCBI Reference Sequences: current status, policy and new initiatives] NAR
# Daniela Puiu [http://genomebiology.com/content/pdf/gb-2008-9-10-r151.pdf A simple, fast, and accurate method of phylogenomic inference] Genome Biology
# Niranjan Nagarajan [http://www.springerlink.com/content/cn3551154w232l73/fulltext.pdf The Stastical Power of Phylogenetic Motif Models] RECOMB 2008
# Sergey Koren [http://www.nature.com/nmeth/journal/v5/n10/full/nmeth1008-903.html Scientific software: seeing the SNPs between us] Nature Methods
# Mohammadreza Ghodsi [http://www.biomedcentral.com/1471-2105/9/386 The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes] BMC Bioinformatics

= 10/27/2008 =
# Bo Liu [http://www.pnas.org/content/105/37/14130.short?rss=1 Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus] PNAS
# Sergey Koren [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn548 Aggressive Assembly of Pyrosequencing Reads with Mates] Bioinformatics
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/21/2431 ZOOM! Zillions of oligos mapped] Bioinformatics
# Mohammadreza Ghodsi [http://www.ncbi.nlm.nih.gov/pubmed/18692931 Biodiversity of the microbial community in a Spanish farmhouse cheese as revealed by culture-dependent and culture-independent methods]

= 11/03/2008 =
# Daniela Puiu [http://genome.cshlp.org/cgi/content/abstract/gr.7088808v1 Short read fragment assembly of bacterial genomes] (Genome Research)

= 11/10/2008 =
# Bo Liu [http://www.pnas.org/content/early/2008/11/04/0802782105.abstract Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility] PNAS

= 11/17/2008 =
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn582 Human genomes as email attachments] Bioinformatics
# Mohammad Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/18/e120 Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers] Nucleic Acids Research
# Sergey Koren [http://www.biomedcentral.com/1471-2105/9/420/abstract XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data] (BMC Bioinformatics)

Pop group meeting

2008-11-17T19:58:36Z

Sergek: /* 11/10/2008 */

Pop group meeting

2008-11-10T00:34:43Z

Sergek:

= 09/29/2008 =

# Benjamin Langmead [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003263 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression] (PLoS one)
# Bo Liu [http://genomebiology.com/2008/9/9/R139 Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues] (Genome Biology)
# Daniela Puiu [http://genome.cshlp.org/cgi/reprint/gr.080200.108v1 Sequencing of natural strains of Arabidopsis thaliana with short reads] (Genome Research)
# Dan Sommer, Niranjan Nagarajan [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)
# James Robert White [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V73-4SHVST0-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=961305&md5=4115e7b8186a36db60f6b11a217a8798 Microbial population dynamics during aerobic sludge granulation at different organic loading rates] (ScienceDirect)
# Mohammad Reza Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/16/5180 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library] (NAR)
# Sergey Koren [http://www.biomedcentral.com/1471-2105/9/390 R/parallel - speeding up bioinformatics analysis with R] (BMC Bioinformatics)
# Theodore Gibbons [http://www.ncbi.nlm.nih.gov/pubmed/18711340 High-resolution metagenomics targets specific functional types in complex microbial communities] (Nature Biotechnology) [http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function] (Systems Microbiology)

= 10/06/2008 =
# Bo Liu [http://www.pnas.org/content/105/39/15076.short The convergence of carbohydrate active gene repertoires in human gut microbes.] PNAS
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/20/2395 SeqMap: mapping massive amount of oligonucleotides to the genome] Bioinformatics
# James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS
# MohammadReza Ghodsi [http://aem.asm.org/cgi/content/abstract/74/5/1453 Metagenomics: Read Length Matters] Applied Environmental Microbiology
# Sergey Koren [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads] PLoS Computational Biology

= 10/13/2008 =
# Daniela Puiu, Daniel Sommer [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003373 MetaSim—A Sequencing Simulator for Genomics and Metagenomics] PLoS ONE
# Bo Liu, James Robert White [http://www.sciencemag.org/cgi/content/full/322/5899/275 Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth.] Science
# MohammadReza Ghodsi [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2557142 Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets] (PLoS one)

MetaSim software:
Location: /fs/sz-user-supported/common/packages/MetaSim/
Executable(Java): /fs/sz-user-supported/common/packages/MetaSim/metasim/MetaSim
Database: /fs/sz-user-supported/common/packages/MetaSim/database
create a symlink to it from your working directory, otherwise you have to import it
NCBI databases: [ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz Complete bacteria]; [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz Taxonomy]

= 10/20/2008 =
# Bo Liu [http://www.pnas.org/content/105/37/13977.short?rss=1 Accelerated evolution of resistance in multidrug environments] PNAS [http://www.pnas.org/content/105/39/14918.short?rss=1 Drug interactions modulate the potential for evolution of resistance] PNAS
# Daniel Sommer [http://www.ncbi.nlm.nih.gov/pubmed/18927115?dopt=Abstract NCBI Reference Sequences: current status, policy and new initiatives] NAR
# Daniela Puiu [http://genomebiology.com/content/pdf/gb-2008-9-10-r151.pdf A simple, fast, and accurate method of phylogenomic inference] Genome Biology
# Niranjan Nagarajan [http://www.springerlink.com/content/cn3551154w232l73/fulltext.pdf The Stastical Power of Phylogenetic Motif Models] RECOMB 2008
# Sergey Koren [http://www.nature.com/nmeth/journal/v5/n10/full/nmeth1008-903.html Scientific software: seeing the SNPs between us] Nature Methods
# Mohammadreza Ghodsi [http://www.biomedcentral.com/1471-2105/9/386 The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes] BMC Bioinformatics

= 10/27/2008 =
# Bo Liu [http://www.pnas.org/content/105/37/14130.short?rss=1 Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus] PNAS
# Sergey Koren [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn548 Aggressive Assembly of Pyrosequencing Reads with Mates] Bioinformatics
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/21/2431 ZOOM! Zillions of oligos mapped] Bioinformatics
# Mohammadreza Ghodsi [http://www.ncbi.nlm.nih.gov/pubmed/18692931 Biodiversity of the microbial community in a Spanish farmhouse cheese as revealed by culture-dependent and culture-independent methods]

= 11/03/2008 =
# Daniela Puiu [http://genome.cshlp.org/cgi/content/abstract/gr.7088808v1 Short read fragment assembly of bacterial genomes] (Genome Research)

= 11/10/2008 =
# Sergey Koren [http://www.biomedcentral.com/1471-2105/9/420/abstract XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data] (BMC Bioinformatics)

Pop group meeting

2008-10-27T14:31:52Z

Sergek:

= 09/29/2008 =

# Benjamin Langmead [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003263 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression] (PLoS one)
# Bo Liu [http://genomebiology.com/2008/9/9/R139 Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues] (Genome Biology)
# Daniela Puiu [http://genome.cshlp.org/cgi/reprint/gr.080200.108v1 Sequencing of natural strains of Arabidopsis thaliana with short reads] (Genome Research)
# Dan Sommer, Niranjan Nagarajan [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)
# James Robert White [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V73-4SHVST0-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=961305&md5=4115e7b8186a36db60f6b11a217a8798 Microbial population dynamics during aerobic sludge granulation at different organic loading rates] (ScienceDirect)
# Mohammad Reza Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/16/5180 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library] (NAR)
# Sergey Koren [http://www.biomedcentral.com/1471-2105/9/390 R/parallel - speeding up bioinformatics analysis with R] (BMC Bioinformatics)
# Theodore Gibbons [http://www.ncbi.nlm.nih.gov/pubmed/18711340 High-resolution metagenomics targets specific functional types in complex microbial communities] (Nature Biotechnology) [http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function] (Systems Microbiology)

= 10/06/2008 =
# Bo Liu [http://www.pnas.org/content/105/39/15076.short The convergence of carbohydrate active gene repertoires in human gut microbes.] PNAS
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/20/2395 SeqMap: mapping massive amount of oligonucleotides to the genome] Bioinformatics
# James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS
# MohammadReza Ghodsi [http://aem.asm.org/cgi/content/abstract/74/5/1453 Metagenomics: Read Length Matters] Applied Environmental Microbiology
# Sergey Koren [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads] PLoS Computational Biology

= 10/13/2008 =
# Daniela Puiu, Daniel Sommer [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003373 MetaSim—A Sequencing Simulator for Genomics and Metagenomics] PLoS ONE
# Bo Liu, James Robert White [http://www.sciencemag.org/cgi/content/full/322/5899/275 Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth.] Science
# MohammadReza Ghodsi [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2557142 Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets] (PLoS one)

MetaSim software:
Location: /fs/sz-user-supported/common/packages/MetaSim/
Executable(Java): /fs/sz-user-supported/common/packages/MetaSim/metasim/MetaSim
Database: /fs/sz-user-supported/common/packages/MetaSim/database
create a symlink to it from your working directory, otherwise you have to import it
NCBI databases: [ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz Complete bacteria]; [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz Taxonomy]

= 10/20/2008 =
# Bo Liu [http://www.pnas.org/content/105/37/13977.short?rss=1 Accelerated evolution of resistance in multidrug environments] PNAS [http://www.pnas.org/content/105/39/14918.short?rss=1 Drug interactions modulate the potential for evolution of resistance] PNAS
# Daniel Sommer [http://www.ncbi.nlm.nih.gov/pubmed/18927115?dopt=Abstract NCBI Reference Sequences: current status, policy and new initiatives] NAR
# Daniela Puiu [http://genomebiology.com/content/pdf/gb-2008-9-10-r151.pdf A simple, fast, and accurate method of phylogenomic inference] Genome Biology
# Niranjan Nagarajan [http://www.springerlink.com/content/cn3551154w232l73/fulltext.pdf The Stastical Power of Phylogenetic Motif Models] RECOMB 2008
# Sergey Koren [http://www.nature.com/nmeth/journal/v5/n10/full/nmeth1008-903.html Scientific software: seeing the SNPs between us] Nature Methods

= 10/27/2008 =

# Sergey Koren [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn548 Aggressive Assembly of Pyrosequencing Reads with Mates] Bioinformatics
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/21/2431 ZOOM! Zillions of oligos mapped] Bioinformatics

Cbcb:Pop-Lab:How-to

2008-09-13T23:14:27Z

Sergek:

==How-To repository==
[http://www.cbcb.umd.edu/intranet/resources.shtml Getting started at the CBCB] 
[[Cbcb:Pop-Lab:AMOS-CVS How to use AMOS through CVS]] 
[[Cbcb:Pop-Lab:AMOScmp-SR How to use AMOScmp with short read data ]] 
How do I annotate a genome at the CBCB? 
[[Cbcb:Pop-Lab:How do I run the new Bambus | How do I run the new Bambus?]] 
How do I use the antibiotic resistance database? 
How do I use the antibiotic resistance database locally? 
How do I run jobs on the grid? 
How do I compare metagenomic datasets through the metastats website? 
How do I compare metagenomic datasets using R directly? 
How do I find CRISPRs in a new genome? 
[[Cbcb:Pop-Lab:SOMA How do I scaffold a genome using optical maps (both locally and through the web) ]] 
How do I generate graph information out of Minimus? 
What tools are available for doing in silico finishing at the CBCB? 
How do I generate a scaffold graph starting from a 454 .ace file? 
How do I draw a pretty picture of a scaffold stored in an AMOS bank?

Cbcb:Pop-Lab:How-to

2008-09-13T23:13:07Z

Sergek:

==How-To repository==
[http://www.cbcb.umd.edu/intranet/resources.shtml Getting started at the CBCB] 
[[Cbcb:Pop-Lab:AMOS-CVS How to use AMOS through CVS]] 
[[Cbcb:Pop-Lab:AMOScmp-SR How to use AMOScmp with short read data ]] 
How do I annotate a genome at the CBCB? 
[[Cbcb:Pop-Lab:How do I run the new Bambus]] 
How do I use the antibiotic resistance database? 
How do I use the antibiotic resistance database locally? 
How do I run jobs on the grid? 
How do I compare metagenomic datasets through the metastats website? 
How do I compare metagenomic datasets using R directly? 
How do I find CRISPRs in a new genome? 
[[Cbcb:Pop-Lab:SOMA How do I scaffold a genome using optical maps (both locally and through the web) ]] 
How do I generate graph information out of Minimus? 
What tools are available for doing in silico finishing at the CBCB? 
How do I generate a scaffold graph starting from a 454 .ace file? 
How do I draw a pretty picture of a scaffold stored in an AMOS bank?

Cbcb:Pop-Lab:How do I run the new Bambus

2008-09-13T23:12:54Z

Sergek:

The new Bambus (aka Bambus 2) actually consists of three executables that run in order using a supplied AMOS bank. An important note, Bambus 2 is still an early beta. As such, it is advisable to back up
the bnk directory before using.

The first program is clk. This program finds all mated reads within contigs and converts the mate distances to be relative to contigs rather than reads. The second program is Bundler. Bundler joins together
the contig link messages generated by clk together when they can be to create consensus links between contigs. It will output multiple contig links for a pair of contigs. The final program is OrientContigs.
OrientContigs uses the contig links to orient and order the contigs into scaffolds, as well as performing some simplification by joining contigs. Each of the programs is covered in more detail below. To get more
help on running any program use -h.

1. clk
- Modifies the bank to create contig edges.
- Example: clk -b[ank] data.bnk

2.Bundler
- Bundle together contig edges to create contig links.
- Example: Bundler -b[ank] data.bnk [-t[ype] comma separated list of edge types]
- The -t[ype] option allows only certain contig edges to be processed. ALL means use any type. The types are defined in src/AMOS/Link_AMOS.hh

3. OrientContigs
- Orient and order the contigs based on the links. This program uses a greedy algorithm to orient and order contigs relative to an arbitrary start contig. Edges that contradict the current scaffold are marked bad
and ignored for the rest of the analysis. They are still output but don't affect any subsequent calculations.

The output is a dot-formatted file as well as an NCBI AGP scaffold format.

Note that this program does not currently linearize the scaffold but maintains them as a graph. This program also recursively simplifies common patters in the graph. Currently the patterns are
bubbles or straight lines. For example, contigs A->B->C will be simplified to just A. Also A->B->D will become A as well. This simplification is performed recursively until the graph is stable. Note that the
\>C/>
simplification updates the bank in a destructive way by removing contigs and replacing them (as well as their edges) with updated contigs. Therefore it is necessary to make a backup of the bank before running

Example: OrientContigs -b[ank] <bank_name> [-a[ll] -[r]noreduce -[n]noagressive]. The -all option specifies whether disconnected contigs should be output as their own scaffolds or if they should be ignored. The -noreduce option
turns off the simplification described above. Finally, the -noaggressive option will mark edges that move a contig more than 3 STDEVS away as bad instead of attempting to reconcile the positions.