Options
flexbar -r reads [-b barcodes] [-a adapters] [options]
Information on software:
-h, --help
Display the help message.
-hh, --full-help
Display the help message with advanced options.
-hm, --man-help
Print advanced options as man document.
-v, --versions
Print Flexbar and SeqAn version numbers.
-c, --cite
Show program reference for citation.
Input read files, output prefix name and multi-threading:
-n, --threads NUM
Number of threads to employ. Default: 1.
-N, --bundle NUM
Number of read pairs per thread. Default: 256.
-t, --target STR
Prefix for output file names or paths. Default: flexbarOut.
-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.
Barcodes are detected, removed and guide the separation of reads:
-b, --barcodes FILE
Fasta file with barcodes for demultiplexing, may contain N.
-b2, --barcodes2 FILE
Additional barcodes file for second read set in paired mode.
-br, --barcode-reads FILE
Fasta/q file containing separate barcode reads for detection.
-be, --barcode-trim-end STR
Type of detection, see section trim-end modes. Default: LTAIL.
-bn, --barcode-tail-length NUM
Region size in tail trim-end modes. Default: barcode length.
-bo, --barcode-min-overlap NUM
Minimum overlap of barcode and read. Default: barcode length.
-bt, --barcode-error-rate NUM
Error rate threshold for mismatches and gaps. Default: 0.0.
-bk, --barcode-keep
Keep barcodes within reads instead of removal.
-bu, --barcode-unassigned
Include unassigned reads in output generation.
-bm, --barcode-match NUM
Alignment match score. Default: 1.
-bi, --barcode-mismatch NUM
Alignment mismatch score. Default: -1.
-bg, --barcode-gap NUM
Alignment gap score. Default: -9.
Adapter sequences are detected and removed if criteria are met:
-a, --adapters FILE
Fasta file with adapters for removal that may contain N.
-a2, --adapters2 FILE
File with extra adapters for second read set in paired mode.
-as, --adapter-seq STR
Single adapter sequence as alternative to adapters option.
-ar, --adapter-read-set STR
Consider only single read set for adapters. One of 1 and 2.
-ac, --adapter-revcomp
Consider also reverse complement of each adapter in search.
-ae, --adapter-trim-end STR
Type of removal, see section trim-end modes. Default: RIGHT.
-an, --adapter-tail-length NUM
Region size for tail trim-end modes. Default: adapter length.
-ad, --adapter-relaxed
Skip restriction to pass read ends in right and left modes.
-ao, --adapter-min-overlap NUM
Minimum overlap of adapter and read for removal. Default: 3.
-at, --adapter-error-rate NUM
Error rate threshold for mismatches and gaps. Default: 0.1.
-am, --adapter-match NUM
Alignment match score. Default: 1.
-ai, --adapter-mismatch NUM
Alignment mismatch score. Default: -1.
-ag, --adapter-gap NUM
Alignment gap score. Default: -6.
Filter and trim reads before and after processing barcodes and adapters:
-u, --max-uncalled NUM
Allowed uncalled bases N 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.
-X, --post-trim-left-hps STR
Trim certain homopolymers on the left read end after removal.
-Y, --post-trim-right-hps STR
Trim certain homopolymers on the right read end after removal.
-Z, --post-trim-hps-length NUM
Minimum length of homopolymers at read ends. Default: 3.
-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.
Trim reads based on sequence quality scores:
-q, --qtrim STR
Quality-based trimming mode. One of TAIL, WIN, and BWA.
-qf, --qtrim-format STR
Quality format. One of sanger, solexa, i1.3, i1.5, and i1.8.
-qt, --qtrim-threshold NUM
Minimum quality as threshold for trimming. Default: 20.
-qw, --qtrim-win-size NUM
Region size for sliding window approach. Default: 5.
-qa, --qtrim-post-removal
Perform quality-based trimming after removal steps.
Select options for output file generation:
-f, --fasta-output
Prefer non-quality format fasta for output.
-z, --zip-output STR
Direct compression of output files. One of GZ and BZ2.
-1, --stdout-reads
Write reads to stdout, tagged and interleaved if needed.
-j, --length-dist
Generate length distribution for read output files.
-s, --single-reads
Write single reads for too short counterparts in pairs.
-S, --single-reads-paired
Write paired single reads with N for short counterparts.
Write alignments to log file or choose read tagging options:
-l, --align-log STR
Print chosen read alignments. One of ALL, MOD, and TAB.
-o, --stdout-log
Write statistics to console instead of target log file.
-g, --removal-tags
Tag reads that are subject to adapter or barcode removal.
-e, --number-tags
Replace read tags by ascending number to save space.
-i, --umi-tags
Capture UMIs in reads at barcode or adapter N positions.
Available trim-end modes for barcodes and adapters:
-
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 -
LTAIL: consider first n bases of reads in alignment -
RTAIL: use only last n bases, see tail-length options