Flash (Fast Length Adjustment of Short Reads)
Provided by: flash_1.2.11-2_amd64 
Proper name
flash - Fast Length Adjustment of Curt reads
SYNOPSIS
flash [OPTIONS] MATES_1.FASTQ MATES_2.FASTQ flash [OPTIONS] --interleaved-input (MATES.FASTQ | -) flash [OPTIONS] --tab-delimited-input (MATES.TAB | -)
DESCRIPTION
Wink (Fast Length Aligning of SHort reads) is an authentic and fast tool to merge paired-end reads that were generated from DNA fragments whose lengths are shorter than twice the length of reads. Merged read pairs effect in unpaired longer reads, which are more often than not more desired in genome assembly and genome analysis processes. Briefly, the FLASH algorithm considers all possible overlaps at or above a minimum length between the reads in a pair and chooses the overlap that results in the lowest mismatch density (proportion of mismatched bases in the overlapped region). Ties betwixt multiple overlaps are broken by considering quality scores at mismatch sites. When building the merged sequence, FLASH computes a consensus sequence in the overlapped region. More details can be found in the original publication (http://bioinformatics.oxfordjournals.org/content/27/21/2957.full). Limitations of FLASH include: - FLASH cannot merge paired-end reads that do not overlap. - Flash is not designed for data that has a meaning amount of indel errors (such as Sanger sequencing data). It is best suited for Illumina data.
MANDATORY INPUT
The about common input to Flash is two FASTQ files containing read 1 and read 2 of each mate pair, respectively, in the same order. Alternatively, y'all may provide 1 FASTQ file, which may be standard input, containing paired-terminate reads in either interleaved FASTQ (run across the --interleaved-input pick) or tab-delimited (run into the --tab-delimited-input selection) format. In all cases, gzip compressed input is autodetected. Too, in all cases, the PHRED outset is, by default, assumed to be 33; utilise the --phred-offset option to modify it.
OUTPUT
The default output of Wink consists of the post-obit files: - out.extendedFrags.fastq The merged reads. - out.notCombined_1.fastq Read 1 of mate pairs that were not merged. - out.notCombined_2.fastq Read 2 of mate pairs that were not merged. - out.hist Numeric histogram of merged read lengths. - out.histogram Visual histogram of merged read lengths. FLASH also logs advisory messages to standard output. These tin can also be redirected to a file, equally in the post-obit example: $ wink reads_1.fq reads_2.fq 2>&one | tee flash.log In addition, Wink supports several features affecting the output: - Writing the merged reads straight to standard output (--to-stdout) - Writing gzip compressed output files (-z) or using an external compression program (--compress-prog) - Writing the uncombined read pairs in interleaved FASTQ format (--interleaved-output) - Writing all output reads to a single file in tab-delimited format (--tab-delimited-output)
OPTIONS
-m, --min-overlap=NUM The minimum required overlap length betwixt two reads to provide a confident overlap. Default: 10bp. -M, --max-overlap=NUM Maximum overlap length expected in approximately 90% of read pairs. It is by default set to 65bp, which works well for 100bp reads generated from a 180bp library, assuming a normal distribution of fragment lengths. Overlaps longer than the maximum overlap parameter are still considered as good overlaps, only the mismatch density (explained below) is calculated over the first max_overlap bases in the overlapped region rather than the entire overlap. Default: 65bp, or calculated from the specified read length, fragment length, and fragment length standard deviation. -ten, --max-mismatch-density=NUM Maximum immune ratio between the number of mismatched base pairs and the overlap length. 2 reads will not be combined with a given overlap if that overlap results in a mismatched base of operations density higher than this value. Annotation: Whatsoever occurence of an 'Northward' in either read is ignored and not counted towards the mismatches or overlap length. Our experimental results suggest that higher values of the maximum mismatch density yield larger numbers of correctly merged read pairs only at the expense of higher numbers of incorrectly merged read pairs. Default: 0.25. -O, --allow-outies Also try combining read pairs in the "outie" orientation, due east.g. Read 1: <----------- Read 2: ------------> as opposed to simply the "innie" orientation, e.g. Read ane: <------------ Read 2: -----------> Flash uses the aforementioned parameters when trying each orientation. If a read pair can be combined in both "innie" and "outie" orientations, the better-fitting one will exist chosen using the aforementioned scoring algorithm that Wink unremarkably uses. This option also causes extra .innie and .outie histogram files to be produced. -p, --phred-get-go=OFFSET The smallest ASCII value of the characters used to represent quality values of bases in FASTQ files. It should be set up to either 33, which corresponds to the afterward Illumina platforms and Sanger platforms, or 64, which corresponds to the earlier Illumina platforms. Default: 33. -r, --read-len=LEN -f, --fragment-len=LEN -s, --fragment-len-stddev=LEN Average read length, fragment length, and fragment standard difference. These are convenience parameters merely, as they are only used for calculating the maximum overlap (--max-overlap) parameter. The maximum overlap is calculated as the overlap of average-length reads from an average-size fragment plus 2.five times the fragment length standard deviation. The default values are -r 100, -f 180, and -s eighteen, and so this works out to a maximum overlap of 65 bp. If --max-overlap is specified, then the specified value overrides the calculated value. If you lot do not know the standard deviation of the fragment library, you can probably assume that the standard deviation is 10% of the average fragment length. --cap-mismatch-quals Cap quality scores assigned at mismatch locations to 2. This was the default behavior in Wink v1.2.7 and earlier. Later versions will instead calculate such scores as max(|q1 - q2|, 2); that is, the accented value of the deviation in quality scores, simply at least 2. Substantially, the new behavior prevents a low quality base telephone call that is likely a sequencing error from significantly bringing down the quality of a high quality, likely correct base call. --interleaved-input Instead of requiring files MATES_1.FASTQ and MATES_2.FASTQ, allow a single file MATES.FASTQ that has the paired-end reads interleaved. Specify "-" to read from standard input. --interleaved-output Write the uncombined pairs in interleaved FASTQ format. -I, --interleaved Equivalent to specifying both --interleaved-input and --interleaved-output. -Ti, --tab-delimited-input Assume the input is in tab-delimited format rather than FASTQ, in the format described below in '--tab-delimited-output'. In this manner you should provide a single input file, each line of which must comprise either a read pair (5 fields) or a single read (3 fields). FLASH will endeavor to combine the read pairs. Single reads will exist written to the output file as-is if as well using --tab-delimited-output; otherwise they will exist ignored. Note that yous may specify "-" as the input file to read the tab-delimited data from standard input. -To, --tab-delimited-output Write output in tab-delimited format (not FASTQ). Each line volition contain either a combined pair in the format 'tag <tab> seq <tab> qual' or an uncombined pair in the format 'tag <tab> seq_1 <tab> qual_1 <tab> seq_2 <tab> qual_2'. -o, --output-prefix=PREFIX Prefix of output files. Default: "out". -d, --output-directory=DIR Path to directory for output files. Default: electric current working directory. -c, --to-stdout Write the combined reads to standard output. In this mode, with FASTQ output (the default) the uncombined reads are discarded. With tab-delimited output, uncombined reads are included in the tab-delimited information written to standard output. In both cases, histogram files are not written, and informational messages are sent to standard error rather than to standard output. -z, --shrink Compress the output files direct with zlib, using the gzip container format. Similar to specifying --shrink-prog=gzip and --suffix=gz, but may be slightly faster. --compress-prog=PROG Pipe the output through the pinch program PROG, which will exist called as `PROG -c -', plus any arguments specified by --compress-prog-args. PROG must read uncompressed data from standard input and write compressed data to standard output when invoked as noted above. Examples: gzip, bzip2, xz, pigz. --compress-prog-args=ARGS A string of boosted arguments that volition be passed to the compression programme if i is specified with --compress-prog=PROG. (The arguments '-c -' are still passed in addition to explicitly specified arguments.) --suffix=SUFFIX, --output-suffix=SUFFIX Utilize SUFFIX as the suffix of the output files after ".fastq". A dot before the suffix is assumed, unless an empty suffix is provided. Default: nil; or 'gz' if -z is specified; or PROG if --shrink-prog=PROG is specified. -t, --threads=NTHREADS Set the number of worker threads. This is in addition to the I/O threads. Default: number of processors. Note: if you need Flash'south output to appear deterministically or in the aforementioned gild equally the original reads, y'all must specify -t 1 (--threads=1). -q, --quiet Exercise not print informational messages. -h, --help Display this assist and exit. -v, --version Display version.
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can exist used for any other usage of the program.
Source: http://manpages.ubuntu.com/manpages/impish/man1/flash.1.html
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