Provided by: flash_1.2.11-2_amd64 
NAME
flash - Fast Length Adjustment of SHort reads
SYNOPSIS
flash [OPTIONS] MATES_1.FASTQ MATES_2.FASTQ
flash [OPTIONS] --interleaved-input (MATES.FASTQ | -)
flash [OPTIONS] --tab-delimited-input (MATES.TAB | -)
DESCRIPTION
FLASH (Fast Length Adjustment of SHort reads) is an accurate 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 result in unpaired longer reads, which are
generally 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 between 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 significant amount of indel errors
(such as Sanger sequencing data). It is best suited for Illumina data.
MANDATORY INPUT
The most common input to FLASH is two FASTQ files containing read 1 and read 2 of each
mate pair, respectively, in the same order.
Alternatively, you may provide one FASTQ file, which may be standard input, containing
paired-end reads in either interleaved FASTQ (see the --interleaved-input option) or
tab-delimited (see the --tab-delimited-input option) format. In all cases, gzip
compressed input is autodetected. Also, in all cases, the PHRED offset is, by default,
assumed to be 33; use the --phred-offset option to change it.
OUTPUT
The default output of FLASH consists of the following 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 informational messages to standard output. These can also be redirected
to a file, as in the following example:
$ flash reads_1.fq reads_2.fq 2>&1 | tee flash.log
In addition, FLASH supports several features affecting the output:
- Writing the merged reads directly 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 between 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, but 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.
-x, --max-mismatch-density=NUM
Maximum allowed ratio between the number of mismatched base pairs and the overlap
length. Two reads will not be combined with a given overlap if that overlap
results in a mismatched base density higher than this value. Note: Any occurence
of an 'N' 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 but 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, e.g.
Read 1: <-----------
Read 2: ------------>
as opposed to only the "innie" orientation, e.g.
Read 1:
<------------
Read 2: ----------->
FLASH uses the same parameters when trying each
orientation. If a read pair can be combined in both "innie" and "outie"
orientations, the better-fitting one will be chosen using the same scoring
algorithm that FLASH normally uses.
This option also causes extra .innie and .outie
histogram files to be produced.
-p, --phred-offset=OFFSET
The smallest ASCII value of the characters used to represent quality values of
bases in FASTQ files. It should be set to either 33, which corresponds to the
later 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 deviation. These are
convenience parameters only, 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 2.5 times the
fragment length standard deviation. The default values are -r 100, -f 180, and -s
18, 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 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 FLASH v1.2.7 and earlier. Later versions will instead calculate such
scores as max(|q1 - q2|, 2); that is, the absolute value of the difference in
quality scores, but at least 2. Essentially, the new behavior prevents a low
quality base 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 mode you should provide a
single input file, each line of which must contain either a read pair (5 fields) or
a single read (3 fields). FLASH will try to combine the read pairs. Single reads
will be written to the output file as-is if also using --tab-delimited-output;
otherwise they will be ignored. Note that you 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 will 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: 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 data 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, --compress
Compress the output files directly with zlib, using the gzip container format.
Similar to specifying --compress-prog=gzip and --suffix=gz, but may be slightly
faster.
--compress-prog=PROG
Pipe the output through the compression program PROG, which will be 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 additional arguments that will be passed to the compression program if
one is specified with --compress-prog=PROG. (The arguments '-c -' are still passed
in addition to explicitly specified arguments.)
--suffix=SUFFIX, --output-suffix=SUFFIX
Use SUFFIX as the suffix of the output files after ".fastq". A dot before the
suffix is assumed, unless an empty suffix is provided. Default: nothing; or 'gz'
if -z is specified; or PROG if --compress-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's output to appear
deterministically or in the same order as the original reads, you must specify -t 1
(--threads=1).
-q, --quiet
Do not print informational messages.
-h, --help
Display this help and exit.
-v, --version
Display version.
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.