NAME

       flexbar - flexible barcode and adapter removal for sequencing platforms

SYNOPSIS

       flexbar -r reads [-t target] [-b barcodes] [-a adapters] [options]

DESCRIPTION

       Flexbar   preprocesses  high-throughput  sequencing  data  efficiently.  It  demultiplexes
       barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are
       provided.   Flexbar   increases  mapping  rates  and  improves  genome  and  transcriptome
       assemblies. It supports next-generation sequencing data in fasta/q  and  csfasta/q  format
       from Illumina, Roche 454, and the SOLiD platform.

       Parameter  names  changed  in  Flexbar.  Please review scripts. The recent months, default
       settings were optimised, several bugs were fixed and various improvements were made,  e.g.
       revamped  command-line  interface,  new  trimming  modes  as well as lower time and memory
       requirements.

       -h, --help

              Displays this help message.

       -w, --advanced

              Print advanced options help screen.

       -i, --cite

              Show program reference for citation.

              Basic options:

       -n, --threads NUM

              Number of threads to employ. Default: 1.

       -t, --target STR

              Prefix for output file names or paths. Default: flexbar.

       -r, --reads FILE

              Fasta/q file or stdin (-) with reads that may contain barcodes.

       -p, --reads2 FILE

              Second input file of paired reads, gz and bz2 files supported.

       -f, --format STR

              Quality format: sanger, solexa, i1.3, i1.5, i1.8 (illumina 1.8+).

       -c, --color-space

              Input in color-space format csfasta or csfastq in sanger scaling.

              Barcode detection:

       -b, --barcodes FILE

              Fasta file with barcodes for demultiplexing that may contain N.

       -br, --barcode-reads FILE

              Fasta/q file composed of separate barcode reads for detection.

       -be, --barcode-trim-end STR

              Type of detection, see section trim-end modes. Default: ANY.

       -bo, --barcode-min-overlap NUM

              Minimum overlap of barcode and read. Default: barcode length.

       -bt, --barcode-threshold NUM

              Allowed mismatches and gaps per 10 bases overlap. Default: 1.0.

       -bu, --barcode-unassigned

              Include unassigned reads in output generation.

              Adapter removal:

       -a, --adapters FILE

              Fasta file with adapters for removal that may contain N.

       -as, --adapter-seq STR

              Single adapter sequence as alternative to adapters option.

       -ae, --adapter-trim-end STR

              Type of removal, see section trim-end modes. Default: RIGHT.

       -ao, --adapter-min-overlap NUM

              Minimum overlap of adapter and read sequence. Default: 1.

       -at, --adapter-threshold NUM

              Allowed mismatches and gaps per 10 bases overlap. Default: 3.0.

              Filtering and trimming:

       -u, --max-uncalled NUM

              Allowed uncalled bases (N or .) for each read. Default: 0.

       -x, --pre-trim-left NUM

              Trim given number of bases on 5' read end before detection.

       -y, --pre-trim-right NUM

              Trim specified number of bases on 3' end prior to detection.

       -q, --pre-trim-phred NUM

              Trim 3' end until specified or higher quality reached.

       -k, --post-trim-length NUM

              Trim to specified read length from 3' end after removal.

       -m, --min-read-length NUM

              Minimum read length to remain after removal. Default: 18.

              Output selection:

       -o, --fasta-output

              Prefer non-quality formats fasta and csfasta for output.

       -z, --zip-output STR

              Enable direct compression of output files. One of GZ and BZ2.

       -s, --single-reads

              Write single paired reads for too short counterparts.

              Logging and tagging:

       -l, --log-level STR

              Print valid optimal read alignment. One of ALL, MOD, and TAB.

       -g, --removal-tags

              Tag reads that are subject to adapter or barcode removal.

              Trim-end modes:

              ANY: longer side of read remains after removal of overlap LEFT: right side  remains
              after  removal,  align <= read end RIGHT: left part remains after removal, align >=
              read start LEFT_TAIL: consider first n bases of reads in alignment RIGHT_TAIL:  use
              only last n bases, see tail-length options

EXAMPLES

              flexbar   -r   reads.fq  -f  i1.8  -t  target  -b  brc.fa  -a  adap.fa  flexbar  -r
              reads.csfastq.gz -a adap.fa -ao 5 -ae LEFT -c

VERSION

              flexbar version: 2.4 Last update July 29, 2013

       Advanced options: flexbar -w

       flexbar version 2.4