FASTQ format

Conversion from 454 sequencer output

Download and use sff_extract, to convert the 454 SFF files to FASTQ format.

sff_extract *.sff -x /dev/null

Conversion from AB1 chromatograms (Sanger)

Sequence files in AB1 format can be batch-converted with the following function using EMBOSS tools, that will use the file name as a read name, and send the FASTQ sequences to the standard output.

function abi2fastq {
       for ABI in *ab1
               seqret -filter abi::$ABI fastq-sanger::stdout |
                       descseq -filter fastq-sanger::stdin fastq-sanger::stdout -name $(basename $ABI .ab1)

This function can be used with commands such as the following example, to be run in the directory containing the chromatogram files. In this example, the name of the FASTQ file is arbitrarily chosen as “library.fastq”.

abi2fastq > library.fastq

Conversion from SRA format (NCBI)

Download and use the SRA Toolkit (available as a Debian package), to convert SRA files to FASTQ format. Example with a file called sequencefile.sra:

fastq-dump sequencefile.sra