Map Reads with Bowtie2 Element
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
string
Reference genome
Path to an indexed reference genome.
reference
string
Output file name
Base name of the output file. ‘out.sam’ by default.
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 allowed in a seed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity.
mismatches_number
numeric
Seed length (–L)
Sets the length of the seed substrings to align. Smaller values make alignment slower but more sensitive.
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.
dpad
numeric
Disallow gaps (–gbar)
Disallow gaps within a specified number of positions of the beginning or end of the read.
gbar
numeric
Seed (–seed)
Use as the seed for pseudo-random number generator.
seed
numeric
Threads
Launch the 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.
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 mixed mode, but will only consider the alignment status of pairs per se, not individual mates.
nomixed
boolean
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.
nodiscordant
boolean
No forward orientation (–nofw)
If –nofw is specified, Bowtie will not attempt to align against the forward reference strand.
nofw
boolean
No reverse-complement orientation (–norc)
If –norc is specified, Bowtie will not attempt to align against the reverse-complement reference strand.
norc
boolean
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.
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.
nocontain
boolean
| Parameter | Description | Default value |
|---|---|---|
| Output directory | Directory to save Bowtie2 output files. | out.sam |
| Reference genome | Path to an indexed reference genome. | |
| Output file name | Base name of the output file. ‘out.sam’ by default. | out.sam |
| Library | Is this library mate-paired? | single-end |
| Mode | Determines valid alignments; includes options -n or -v for mismatches. | –end-to-end |
| Number of mismatches | Sets allowed mismatches in a seed alignment. | 0 |
| Seed length | Length of seed substrings to align. Smaller values increase sensitivity but slow down alignment. | 20 |
| Add columns for gaps | Pad dynamic programming columns for allowing gaps. | 15 |
| Disallow gaps | Prevent gaps within specified positions from read ends. | 4 |
| Seed | Seed for pseudo-random number generator. | 0 |
| Threads | Number of parallel threads. Speedup is close to linear with more threads. | 1 |
| No unpaired alignments | Disable mixed mode in paired-end alignments. | False |
| No discordant alignments | Disable searching for discordant alignments. | False |
| No forward orientation | Prevent alignment against forward reference strand. | False |
| No reverse-complement orientation | Prevent alignment against reverse-complement reference strand. | False |
| No overlapping mates | Consider overlapping mates as non-concordant. | False |
| No mates containing one another | Consider mates containing each other as non-concordant. | False |
Input/Output Ports
The element has 1 input port:
Name in GUI: Bowtie2 data
Name in Workflow File: in-data
Slots:
- URL of a file with mate reads
- readsurl
string
- URL of a file with reads
- readspairedurl
string
And 1 output port:
Name in GUI: Bowtie2 output data
Name in Workflow File: out-data
Slots:
- Assembly URL
- assembly-out
string