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 requirements.
- Displays this help message.
- Print advanced options help screen.
- 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+).
- 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.
- 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:
- 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.
- 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
- 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