Performs alignment of short reads with Bowtie2.
Element type: align-reads-with-bowtie2
Parameters in GUI
|Output directory||Directory to save Bowtie2 output files.||output-dir|
|Reference genome||Path to an indexed reference genome.||reference||string|
|Output file name||Base name of the output file. 'out.sam' by default.||out.sam||outname||string|
|Library||Is this library mate-paired?||single-end||library||string|
|Mode||When the -n option is specified (which is the default), bowtie determines which alignments are valid according to the following policy, which is similar to Maq's default policy. In -v mode, alignments may have no more than V mismatches, where V may be a number from 0 through 3 set using the -v option. Quality values are ignored. The -v option is mutually exclusive with the -n option.||--end-to-end||mode||string|
|Number of mismatches|
Sets the number of mismatches to allowed in a seed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity.
|Seed length (--L)||Sets the length of the seed substrings to align. Smaller values make alignment slower but more senstive.||20||seed_len||numeric|
|Add columns to allow gaps (--dpad)||"Pads" dynamic programming problems by the specified number of columns on either side to allow gaps.||15||dpad||numeric|
|Disallow gaps (--gbar)|
Disallow gaps within a specified number of positions of the beginning or end of the read.
|Seed (--seed)||Use as the seed for pseudo-random number generator.||0||seed||numeric|
|Threads||Launch specified number of parallel search threads. Threads will run on separate processors/cores and synchronize when parsing reads and outputting alignments. Searching for alignments is highly parallel, and speedup is close to linear.||1||threads||numeric|
|No unpaired alignments (--no-mixed)|
If Bowtie2 cannot find a paired-end alignment for a pair, by default it will go on to look for unpaired alignments for the constituent mates. This is called "mixed mode." To disable mixed mode, set this option. Bowtie2 runs a little faster in the mixed mode, but will only consider the alignment status of pairs per se, not individual mates.
|No discordant alignments (--no-discordant)||By default, Bowtie2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints. This option disables that behavior.||False||nodiscordant||boolean|
|No forward orientation (--nofw)||If --nofw is specified, bowtie will not attempt to align against the forward reference strand.||False||nofw||boolean|
|No reverse-complement orientation (--norc)|
If --norc is specified, bowtie will not attempt to align against the reverse-complement reference strand.
|No overlapping mates (--no-overlap)||If one mate alignment overlaps the other at all, consider that to be non-concordant. Default: mates can overlap in a concordant alignment.||False||nooverlap||boolean|
|No mates containing one another (--no-contain)||If one mate alignment contains the other, consider that to be non-concordant. Default: a mate can contain the other in a concordant alignment.||False||nocontain||boolean|
|Parameter in Workflow File||Type|
The element has 1 input port:
Name in GUI: Bowtie2 data
Name in Workflow File: in-data
|URL of a file with mate reads||readsurl||string|
|URL of a file with reads||readspairedurl||string|
Slot In GUI
Slot in Workflow File
And 1 output port:
Name in GUI: Bowtie2 output data
Name in Workflow File: out-data
Slot In GUI
Slot in Workflow File