FAR

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Category

Bioinformatics

Program On

zcluster

Version

2.15

Author / Distributor

Please see http://sourceforge.net/projects/theflexibleadap/ and http://sourceforge.net/apps/mediawiki/theflexibleadap/

Description

FAR (The Flexible Adapter Remover) is a program that removes adapter sequences from deep sequencing data in FASTA/Q, CSFASTA/Q format (Illumina / Roche 454 / SOLiD Colorspace). It also demultiplexes barcoded runs. Please see http://sourceforge.net/projects/theflexibleadap/ and http://sourceforge.net/apps/mediawiki/theflexibleadap/

Running Program

Version 2.15 is installed in /usr/local/far/2.15 and /usr/local/far/latest points to the latest installed version. There is a symbolic link to the binary far in /usr/local/bin, so this binary can be invoked without specifying its full path.

Also refer to Running Jobs on zcluster Example of a shell script sub.sh to run on at the batch queue:

 #!/bin/bash
 cd working_directory
 far [options] 

Example of submission to the queue:

 qsub -q queuename   ./sub.sh 

Documentation

Please see far

far
Usage: Flexible Adapter Remover, version 2.15  [OPTION]... 

  -h,        --help                 displays this help message
  -v,        --version              return program version
  -s,        --source               input file
  -s2,       --source2              second input file (if paired run)
  -t,        --target               output file
  -f,        --format               input file format - fastq (=fastq-illumina15), fastq-illumina13, fastq-sanger, fastq-solexa, fasta,csfastq,csfasta default is fasta, output will be in the same format
  -a,        --adapters             FASTA file with adaptersequences to be removed (will try subsequently, but only remove one). 
  -b,        --barcodes             FASTA file with barcode sequences. 
  -br,       --barcode-reads        FASTA/Q file with barcode sequences. Leave empty if barcodes are within the reads. 
  -bm,       --barcode-mismatch     Allowed mismatches for a barcode  (default 1)
  -bmo,      --barcode-min-overlap  Minimum required overlap between known barcode and barcode sequence (default: barcode length - 1 )
  -be,       --barcode-trim-end     If you specify this option the barcode is assumed to be within the read. Trim options are  to --trim-end: left/right/any 
  -do,       --demultiplex-only     yes/no (if set to yes only barcode classification will be done.) (default no)
  -as,       --adapter              String to be removed (alternative to --adapters option). 
  -alg,      --algorithm            needlemanQuality (quality based global alignment via needleman wunsch quality alignment) or needleman (complete global overlap alignment via needleman wunsch) (default needleman)
  -pre,      --fixed-pre-trim       if set, trims the reads to the number of specified bases before alignment (default -1)
  -ao,       --adaptive-overlap     If set to 'yes' the parameter '--min-overlap' will be treated as adaptive measure (see docs, default: no)
  -post,     --fixed-post-trim      if set, trims the reads to the number of specified bases after alignment (default -1)
  -phredpre, --phred-pre-trim       if set, trims the reads to the length were phred/sanger (scaling depends on --format setting) quality will be bigger than this value (searching from 3' end of reads) (default -1)
  -end,      --trim-end             Decides which type of adapterremoval is performed. Modes: 
 right - adapter is removed if adapter aligns >= read start position 
 left - adapter is removed if adapter aligns <= read end position 
 any - adapter is removed if adapter aligns, longer part of read remains 
 left_tail - adapter is searched only in the first n bases of the read (n = adapterlength) 
 right_tail - adapter is searched only in the last n bases of the read (n = adapterlength) (default right)
  -c,        --cut-off              Max. nr of allowed mismatches + indels for alignment per 10 bases  (default 2)
  -o,        --min-overlap          minimum required overlap of adapter and sequence in basepairs  (default 10)
  -ml,       --min-readlength       minimum readlength in basepairs after adapter removal - read will be discarded otherwise  (default 18)
  -of,       --omitted-reads-file   File which contains reads, that were to short after adapter removal according to min-readlength. (default: input_file.omitted)
  -u,        --max-uncalled         nr of allowed uncalled bases in a read (might be a '.' or an 'N').  (default 0)
  -sm,       --match                match score  (default 3)
  -sf,       --mismatch             mismatch penalty  (default -3)
  -sg,       --gap-cost             gap penalty  (default -20)
  -th,       --nr-threads           Number of threads to use  (default 1)
  -l,        --log-level            Report detailed Alignment information: 
 ALL: Full alignment for each read 
 CHANGED: Alignments of reads where adapters have been removed 
 TAB: Same as changed, but TAB-wise output. 
 This will slow down the processing!  (default NONE)
  -n,        --modified-tag         All reads which are modified by FAR will have a colon followed by this tag in their readname. (default NONE)
  -d,        --write-lengthdist     Writes a length distribution to the specified filename. By default it is: <targetfilename>.lengthdist (Options: yes/no) (default yes)

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Installation

Pre-compiled binary downloaded from http://sourceforge.net/projects/theflexibleadap/ and installed in /usr/local/far/2.15. There is a symbolic link to the binary far in /usr/local/bin, so this binary can be invoked without specifying its full path.

System

64-bit Linux