Fastx-Toolkit on Helix
Fastx-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
How To Use
helix $ /usr/local/fastx_toolkit/fastq_to_fasta -h
usage: fastq_to_fasta [-h] [-r] [-n] [-v] [-z] [-i INFILE] [-o OUTFILE]
Part of FASTX Toolkit 0.0.13 by A. Gordon (firstname.lastname@example.org)
[-h] = This helpful help screen.
[-r] = Rename sequence identifiers to numbers.
[-n] = keep sequences with unknown (N) nucleotides.
Default is to discard such sequences.
[-v] = Verbose - report number of sequences.
If [-o] is specified, report will be printed to STDOUT.
If [-o] is not specified (and output goes to STDOUT),
report will be printed to STDERR.
[-z] = Compress output with GZIP.
[-i INFILE] = FASTA/Q input file. default is STDIN.
[-o OUTFILE] = FASTA output file. default is STDOUT.
helix $ /usr/local/fastx_toolkit/fastq_to_fasta -i inputFile -o outputFile