HPC:FASTX-Toolkit
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FASTX-Toolkit
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. FASTX-Toolkit v0.0.14 is installed across all HPC nodes.
Usage
The FASTX-Toolkit can be loaded as a module
[asrini@node061 ~]$ module show fastx_toolkit-0.0.14
-------------------------------------------------------------------
/usr/share/Modules/modulefiles/fastx_toolkit-0.0.14:
module-whatis The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
prepend-path PATH /opt/software/fastx_toolkit/0.0.14/bin/
-------------------------------------------------------------------
[asrini@node061 ~]$ module load fastx_toolkit-0.0.14
[asrini@node061 ~]$ which fastx_trimmer
/opt/software/fastx_toolkit/0.0.14/bin/fastx_trimmer
[asrini@node061 ~]$ fastx_trimmer -h
usage: fastx_trimmer [-h] [-f N] [-l N] [-t N] [-m MINLEN] [-z] [-v] [-i INFILE] [-o OUTFILE]
Part of FASTX Toolkit 0.0.14 by A. Gordon (assafgordon@gmail.com)
[-h] = This helpful help screen.
[-f N] = First base to keep. Default is 1 (=first base).
[-l N] = Last base to keep. Default is entire read.
[-t N] = Trim N nucleotides from the end of the read.
'-t' can not be used with '-l' and '-f'.
[-m MINLEN] = With [-t], discard reads shorter than MINLEN.
[-z] = Compress output with GZIP.
[-i INFILE] = FASTA/Q input file. default is STDIN.
[-o OUTFILE] = FASTA/Q output file. default is STDOUT.
