kingfisher extract

DESCRIPTION

Extract .sra format files into FASTQ or FASTA format, compressed or uncompressed.

OPTIONS

EXTRACTION OPTIONS

--sra SRA

Extract this SRA file [required]

--output-directory OUTPUT_DIRECTORY

Output directory to write to [default: current working directory]

-f, --output-format-possibilities {sra,fastq,fastq.gz,fasta,fasta.gz} [{sra,fastq,fastq.gz,fasta,fasta.gz} ...]

Allowable output formats. If more than one is specified, downloaded data will processed as little as possible [default: "fastq fastq.gz"]

--force

Re-download / extract files even if they already exist [default: Do not].

--unsorted

Output the sequences in arbitrary order, usually the order that they appear in the .sra file. Even pairs of reads may be in the usual order, but it is possible to tell which pair is which, and which is a forward and which is a reverse read from the name [default: Do not].

Currently requires download from NCBI rather than ENA.

--stdout

Output sequences to STDOUT. Currently requires --unsorted [default: Do not].

-t, --threads THREADS

Number of threads to use for extraction [default: 8]

OTHER GENERAL OPTIONS

--debug

output debug information

--version

output version information and quit

--quiet

only output errors

--full-help

print longer help message

--full-help-roff

print longer help message in ROFF (manpage) format

AUTHOR

Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology <benjwoodcroft near gmail.com>

EXAMPLES

Extract an SRA file to FASTQ.GZ format using 16 threads (default is 8)

$ kingfisher extract --sra ERR1739691.sra -t 16 -f fastq.gz