Flash (Fast Length Adjustment of Short Reads)

Provided by: flash_1.2.11-2_amd64 bug

        

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.        

lewisadmily.blogspot.com

Source: http://manpages.ubuntu.com/manpages/impish/man1/flash.1.html

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