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