Map Reads with Bowtie Element
This page provides information on performing alignment of short reads using Bowtie.
Element type: align-reads-with-bowtie
Parameters
| Parameter | Description | Default value | Type |
|---|---|---|---|
| Output directory | Directory to save Bowtie output files. | string | |
| output-dir | Directory path for saving output files. | string | |
| Reference genome | Path to an indexed reference genome. | string | |
| reference | Path location of the reference genome. | string | |
| Output file name | Base name of the output file. By default, it is ‘out.sam’. | out.sam | string |
| Library | Specifies if the library is mate-paired. | single-end | string |
| Mode | Determines the valid alignments policy. In -v mode, alignments may have no more than V mismatches, where V is a number from 0 through 3. Quality values are ignored. The -v option is mutually exclusive with the -n option. | -n mode | string |
| mismatches_type | Alignment policy type according to the mismatches. | -n mode | string |
| Mismatches number | Number of mismatches allowed. | 2 | numeric |
| maqerr | Maximum permitted sum of quality values at mismatched read positions throughout the alignment. Default is 70. | 70 | numeric |
| Seed length | Number of bases on the high-quality end of the read for the -n ceiling to apply. Faster for larger values. | 28 | numeric |
| seedLen | Length of the seed. | 28 | numeric |
| Maximum of backtracks | Maximum insert size for valid paired-end alignments. With a default of 250. | 800 | numeric |
| maxbts | Maximum backtrack setting. | 800 | numeric |
| Best hits | Amount of memory in megabytes provided to store path descriptors in –best mode. Default is 64. | 64 | numeric |
| chunkmbs | Memory allocation for best hits. | 64 | numeric |
| Seed | Seed for pseudo-random number generator. | 0 | numeric |
| Colorspace | When -C is specified, read sequences are treated as colors. | False | boolean |
| No Maq rounding | Disables rounding of quality values in the Phred quality scale. | False | boolean |
| No forward orientation | Prevents alignment against the forward reference strand. | False | boolean |
| No reverse-complement orientation | Prevents alignment against the reverse-complement reference strand. | False | boolean |
| Try as hard | Attempts to find all valid alignments, including paired-end alignments. Useful but slower than default. | False | boolean |
| Best alignments | Guarantees reported singleton alignments are best in terms of mismatches and quality values. Slower operation when specified. | False | boolean |
| All alignment | Reports all valid alignments per read or pair. | False | boolean |
Input/Output Ports
The element has 1 input port:
Name in GUI: Bowtie data
Name in Workflow File: in-data
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| URL of a file with mate reads | readsurl | string |
| URL of a file with reads | readspairedurl | string |
And 1 output port:
Name in GUI: Bowtie output data
Name in Workflow File: out-data
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Assembly URL | assembly-out | string |