Author / Distributor
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/
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
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)
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.