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flexbar - flexible barcode and adapter removal for sequencing platforms
flexbar -r reads [-t target] [-b barcodes] [-a adapters] [options]
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
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Print advanced options help screen.
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-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+).
Input in color-space format csfasta or csfastq in sanger scaling.
-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.
Include unassigned reads in output generation.
-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.
Prefer non-quality formats fasta and csfasta for output.
-z, --zip-output STR
Enable direct compression of output files. One of GZ and BZ2.
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.
Tag reads that are subject to adapter or barcode removal.
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
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
flexbar version: 2.4 Last update July 29, 2013
Advanced options: flexbar -w
flexbar version 2.4
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