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 v 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.


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