Cbcb - User contributions [en]

Cbcb:Pop-Lab:Ben-Report

2009-02-16T15:38:32Z

Langmead:

'''Recent work.'''

Snapshot:

I'm working hard on getting paired-end support into Bowtie. I've settled on the best technique for doing this and I've implemented it in the -v 0 and -v 1 (no mismatches, one-mismatch resp.) alignment modes. I am now testing it, hoping to release a new version of Bowtie in the next couple days.

Outline of future work:

* Bowtie
** Paired-end support
*** Settled on a "mixed-mode" paradigm: find anchor mates in BW space, find opposite mates in reference space
**** Index becomes larger to accommodate the reference text (2.2 GB -> 2.9 GB for human)
**** Speed is about 2x slower than if all the mates were aligned in single-end mode
**** Default mode is "best-effort" - if you want Bowtie to bend over backwards to report all non-concordant pairs, that will be much slower but it can be activated from the command line
** Gapped alignment
** Mapping qualities
*** A la Maq
** Color space
* Crossbow
** Already have some results using some 1000-Genomes data: about 1 hr to align about 14.5x coverage for human
** Would like to do another run that includes paired-end reads and for which there is a trusted set of called SNPs

Cbcb:Pop-Lab

2009-02-16T15:32:21Z

Langmead: /* Progress Reports */

= 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:Ben-Report|Ben]]
* [[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

2008-12-08T21:04:25Z

Langmead: /* 12/1/2008 */

= 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)
# Ted 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
# Mohammad Reza 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 =
# Bo Liu [http://bioinformatics.oxfordjournals.org/cgi/content/short/24/22/2579?rss=1 Phylogenetic distances are encoded in networks of interacting pathways] Bioinformatics
# 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)
# James Robert White [http://www.pnas.org/content/early/2008/08/08/0801925105.abstract?etoc Resistance, resilience, and redundancy in microbial communities] PNAS

= 11/24/2008 =
# Ted Gibbons [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0060295 Gut Reaction: Pyrosequencing Provides the Poop on Distal Gut Bacteria (summary)] PLoS [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0060280 The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing] PLoS [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000255 Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing] PLoS Genetics

= 12/1/2008 =
# Mohammad Ghodsi [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0002836 Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing] PLoS ONE
# Ben Langmead [http://www.sciencemag.org/cgi/rapidpdf/1162986v1.pdf Real-Time DNA Sequencing from Single Polymerase Molecules], Science

Cbcb:Pop-Lab:Members

2008-09-28T14:58:56Z

Langmead:

==Pop-lab group members ==
[http://www.cbcb.umd.edu/~mpop Mihai Pop] - the big Kahuna 
[http://www.cbcb.umd.edu/~niranjan Niranjan Nagarajan] - postdoctoral fellow 
Dan Sommer - bioinformatics engineer 
[http://www.cs.umd.edu/~ghodsi MohammadReza Ghodsi] - graduate student ([http://www.cs.umd.edu CS]) 
[http://www.cs.umd.edu/~sergek Sergey Koren] - graduate student ([http://www.cs.umd.edu CS]) 
[http://www.cbcb.umd.edu/~boliu Bo Liu] - graduate student ([http://cbmg.umd.edu CBMG]) 
[http://www.cbcb.umd.edu/~whitej James White] - graduate student ([http://amsc.umd.edu AMSC]) 
[http://www.cbcb.umd.edu/~langmead/index.html Ben Langmead] - graduate student ([http://www.cs.umd.edu CS])

Cbcb:Pop-Lab:Members

2008-09-28T14:58:20Z

Langmead:

==Pop-lab group members ==
[http://www.cbcb.umd.edu/~mpop Mihai Pop] - the big Kahuna 
[http://www.cbcb.umd.edu/~niranjan Niranjan Nagarajan] - postdoctoral fellow 
Dan Sommer - bioinformatics engineer 
[http://www.cs.umd.edu/~ghodsi MohammadReza Ghodsi] - graduate student ([http://www.cs.umd.edu CS]) 
[http://www.cs.umd.edu/~sergek Sergey Koren] - graduate student ([http://www.cs.umd.edu CS]) 
[http://www.cbcb.umd.edu/~boliu Bo Liu] - graduate student ([http://cbmg.umd.edu CBMG]) 
[http://www.cbcb.umd.edu/~whitej James White] - graduate student ([http://amsc.umd.edu AMSC]) 
[http://www.cbcb.umd.edu/~langmead Ben Langmead] - graduate student([http://www.cs.umd.edu CS])

Cbcb:Pop-Lab:Software

2008-09-28T14:50:02Z

Langmead:

==Software developed by members of our group==
[http://amos.sourceforge.net AMOS] - open-source assembly package 
[http://amos.sourceforge.net/docs/bambus Bambus] - hierachical genome scaffolder 
[http://amos.sourceforge.net/Figaro Figaro] - sequence trimmer that does not require knowledge about the vector sequence 
[http://www.cbcb.umd.edu/~whitej/metastats/detection.shtml MetaStats] - statistical methods for comparing metagenomic samples 
[http://www.cbcb.umd.edu/soma On-Soma] - scaffolder for optical mapping data 
[http://ardb.cbcb.umd.edu ARDB] - antibiotic resistance database 
[http://bowtie-bio.sourceforge.net Bowtie] - ultrafast and memory-efficient short read aligner 
Prokaryotic annotation pipeline 
Comparative annotation viewer