User:Dpuiu: Difference between revisions

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* assemble into 5 contigs by velvet.sh            (velveth)
* assemble into 5 contigs by velvet.sh            (velveth)
* Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.subset.fa
* Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.subset.fa
'''Solexa & 454'''
* [http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP001087 E coli Whole Genome Sequencing on 454 and Illumina]

Revision as of 21:03, 15 December 2009

Daniela Puiu's page

Bookmarks

NCBIsub ; wPip ; Definitions ; Pop ; Perl ; C ; Linux

NCBI

Links

Projects

DHS genomes

Other genomes

Other

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