Splazers

Options

version-check

Turn this option off to disable version update notifications of the application.

forward

only compute forward matches

reverse

only compute reverse complement matches

percent-identity

Percent identity threshold.

recognition-rate

set the percent recognition rate

param-dir

Read user-computed parameter files in the directory <DIR>.

indels

Allow indels. Default: mismatches only.

library-length

Paired-end library length.

library-error

Paired-end library length tolerance.

max-hits

Output only <NUM> of the best hits.

unique

Output only unique best matches (-m 1 -dr 0 -pa).

trim-reads

Trim reads to given length. Default: off.

min-clipped-len

min. read length for read clipping

quality-in-header

quality string in fasta header

verbose

verbose mode

vverbose

very verbose mode

alignment

dump the alignment for each match

purge-ambiguous

purge reads with more than max-hits best matches

distance-range

only consider matches with at most NUM more errors compared to the best (default output all)

output-format

Set output format. 0 = RazerS, 1 = Enhanced Fasta, 2 = Eland, 3 = GFF, 4 = SAM.

genome-naming

Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1.

read-naming

Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1.

sort-order

Select how matches are sorted. 0 = read number, 1 = genome position.

position-format

Select begin/end position numbering (see Coordinate section below). 0 = gap space, 1 = position space.

split-mapping

min. match length for prefix/suffix mapping (to disable split mapping, set to 0)

max-gap

max. length of middle gap

min-gap

min. length of middle gap (for edit distance mapping about 10% of read length is recommended)

errors-prefix

max. number of errors in prefix match

errors-suffix

max. number of errors in suffix match

genome-len

genome length in Mb, for computation of expected number of random matches

anchored

anchored split mapping, only unmapped reads with mapped mates will be considered, requires the reads to be given in SAM format

penalty-c

percent of read length, used as penalty for split-gap

overabundance-cut

Set k-mer overabundance cut ratio.

repeat-length

Skip simple-repeats of length <NUM>.

taboo-length

Set taboo length.

low-memory

decrease memory usage at the expense of runtime

match-N

N matches all other characters. Default: N matches nothing.

error-distr

Write error distribution to FILE.

Views

Splazers Std Output

The text sent to standard out during the execution of Splazers.

Splazers Error Output

The text sent to standard error during the execution of Splazers. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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