User:Dpuiu: Difference between revisions
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* [[Vector_trimming|Vector trimming]] | * [[Vector_trimming|Vector trimming]] | ||
* [[Data_formats|Data formats]] | * [[Data_formats|Data formats]] | ||
* [[dpuiu_definitions|Definitions]] | * [[dpuiu_definitions|Definitions]] | ||
* [[dpuiu_meeting_notes|Meeting notes]] | * [[dpuiu_meeting_notes|Meeting notes]] | ||
| Line 95: | Line 94: | ||
* [[dpuiu_snp|Snp calling]] | * [[dpuiu_snp|Snp calling]] | ||
* [[dpuiu_todo|ToDo]] | * [[dpuiu_todo|ToDo]] | ||
* [[dpuiu_JHU|JHU]] | |||
= CBCB software = | = CBCB software = | ||
Revision as of 18:12, 24 June 2011
Daniela Puiu's page
Bookmarks
Perl ; C ; Linux; Windows; R; BioPerl HOWTOs; CBCB computers
NCBI
- NCBI ; AA ; BLAST ; Microbial_Genomes ; SRA SRA_FTP ; TA ; TA_FTP ; Genomes_FTP ; Bacterial Genomes FTP ; Taxonomy CommonTree
- Complete Bacteria
Links
- Baylor
- EMBL
- EMBOSS
- Homo Sapiens Genome Projects
- JGI Microbial Genomes
- JGI Genomes Online (GOLD)
- JGI Integrated Microbial Genomes (IMG)
- Sanger
- Sanger Microbial Genomes
- CBCB
- NCBI complete genomes: /fs/szdata//ncbi/genomes/Bacteria/ (*.fna)
- www -> /fs/www-cbcb/htdocs/
- Personal web site http://www.cbcb.umd.edu/~dpuiu -> /fs/www/users/dpuiu/
- Personal ftp site ftp://ftp.cbcb.umd.edu/pub/data/dpuiu -> /fs/ftp-cbcb/pub/data/dpuiu/
- ARKDB genetic maps - cow, chicken ...
Projects
DHS genomes
- Bioterrorism
- Bacillus anthracis
- Burkholderia mallei
- Burkholderia pseudomallei
- Clostridium botulinum (Hall strain A str. ATCC 3502) ; uploaded to Insignia ; (other) ; some uploaded to Insignia
- Clostridium perfringens ; some uploaded to Insignia
- Cryptosporidium hominis (test)
- Francisella tularensis OSU18 in Insignia
- Francisella tularensis some uploaded to Insignia
- Salmonella (Washington Univ in St Louis)
- Yersinia enterocolitica
- Yersinia pestis
Other genomes
- Bombus impatiens
- Brugia malayi
- Bos taurus , Bos taurus redo , Bos taurus 3.0
- Cat
- Coffee BACs
- Culex pipiens wolbachia symbiont
- Culex pipiens wolbachia mitochondrion
- Helicobacter pylori
- Homo sapiens
- Kalanchoe
- Megachile rotundata
- Methanobrevibacter smithii
- Pine tree
- Pseudomonas aeruginosa
- Pseudomonas syringae
- Sea urchin
- Turkey
- Xanthomonas oryzae XOO
- Xanthomonas campestris pv. raphani XCR
- Strawberry
Other
- Sequencing
- Alignment *
- CA ; Assembly
- Assemblathon
- HTS
- Comparative assemblies
- Metagenomics
- NCBI submission
- Repeat search
- Vector trimming
- Data formats
- Definitions
- Meeting notes
- My articles
- CS ; Perl ; C ; Linux ; DOS ; wiki ; thunderbird
- Pop group meeting (Monday 's 3pm)
- Snp calling
- ToDo
CBCB software
- Link
https://wiki.umiacs.umd.edu/cbcb/index.php/Communal_Software#Core_Software
- Locations
/fs/szdevel/core-cbcb-software /fs/sz-user-supported
- Change group
$ groups
dpuiu cbcb-staff cbcb cbcbwww
$ newgroup cbcb-staff
# creates a new shell;
$ ^D
- After install ...
find /fs/szdevel/core-cbcb-software | xargs chgrp cbcb-staff find /fs/szdevel/core-cbcb-software | xargs chmod o-w
Test data sets
Sanger (1)
- 23,536 reads ; 11,652 mates; 1 lib : 4.5K mean; 7X cvg
- Location: /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G878A1.frg
Sanger (2)
- 100,781 reads ; 50,008 mates; 24 libs : 4.5K & 10K means; 16X cvg
- Location: /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G*frg
Solexa unpaired
- 2,659,250 36bp reads
- Location: /fs/szdata/Solexa/Streptococcus_suis/suisp17/strip3.fna
Solexa paired (1)
- 142,858 35bp reads;
- assemble into one 99,995 ctg/scaff by velvet
- Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.fa
Solexa paired (2)
- 92,143 35bp reads;
- assemble into 1 scaff by velvetp.sh (velveth -shortPaired)
- assemble into 5 contigs by velvet.sh (velveth)
- Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.subset.fa
Solexa & 454
- E coli Whole Genome Sequencing on 454 and Illumina
- Location /fs/szattic-asmg4/dpuiu/Ecoli