Formats and standards for sequencing data

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Formats and standards for sequencing data
Matúš Kalaš INF389, CBU, BCCS/UiB, Bergen Nov 12,
2010
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SHRiMP Maq BWA Bowtie RMAP Eland SOAP SOAP2 MOSAIK
SOCS PatMaN ZOOM PASS PerM RazerS segemehl MPSCAN
BFAST Lastz BLAT
454 Solexa/Illumina SOLiD
Genome Metagenome Gene annotation Gene
expression Binding sites Variation
Celera Newbler Velvet Euler SOAPdenovo
GenBank EMBL DDBJ Genome Catalogue SNPdb
NCBI SRA EMBL-EBI ENA Your databases
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454 output formats
.sff .fna .qual
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Illumina output formats
.seq.txt .prb.txt Illumina FASTQ (ASCII
64 is Illumina score) Qseq (ASCII 64 is Phred
score) Illumina single line format SCARF
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SOLiD output format(s)
CSFASTA
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Real (standard) FASTQ Sanger
FASTQ (ASCII 33 is Phred score)

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Example of dealing with diverse read formats

in Galaxy
(http//usegalaxy.org)
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If reads should be deposited in a public
repository

SRA (Short Read Archive) at NCBI ENA at EMBL-EBI
SRA format (XML) SRF format
Or should they be deleted?
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Common (standard) format for read alignments

SAM BAM ( binary SAM)
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Some common formats for results (Genome/Gene
annotation)

BED format (genome-browser tracks) GFF
format (gene/genome features) BioXSD (XML)
(any annotation under development)
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Deposit genome/metagenome in a public repository

INSDC databases GenBank, EMBL, DDBJ
Deposit genome/metagenome metadata
MIGS/MIMS standard by GSC
GCDML format (XML) (under development) following
the MIGS/MIMS standard
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MIGS Minimum Information about a Genome
SequenceMIMS Minimum Information about a
Metagenome Sequence/Sample

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MIGS/MIMS checklist

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MIGS/MIMSmetadata example

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Sequencing experiment metadata

MINSEQE standard by FGED Minimum Information
about a high-throughput Nucleotide SEQuencing
Experiment (under development)
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Take-home messages

• Use raw sequencing data when possible
• For base-call data, use standard FASTQ
  (Sanger, Phred)
• For read alignments, use SAM/BAM format
• Use common formats for your results (e.g. GFF or
  BED format)
• Hope for new, generic, extensible standard
  format(s)
• Submit MIGS/MIMS-compliant metadata of genome
  sequences
• Keep an eye on MINSEQE standard, store your
  sequencing metadata