Tools for working with genomic and high throughput sequencing data.
Group: SAM/BAM
Find reads that are from technical or synthetic sequences in a BAM file. Takes in a BAM file, extracts the read pairs and fragment reads that are unmapped, and tests them to see if they are likely generated from a technical sequence (e.g. adapter dimer).
The identification of reads is done by testing the first N bases (controlled by the
match-length parameter) of each read against all sub-sequences of length N from the
technical sequences. Sub-sequences are generated from both the sequences and the
reverse complement of the sequences, ignoring any sub-sequences that include Ns.
By default the output BAM file will contain all reads that matched to a sub-sequence of the technical sequences and, if the read is paired, the read’s mate pair. An option is available to apply a tag to matched reads (–tag/-t), and if specified each matching read will be tagged with the 0-based index of the sequence to which it matched. In combination with tagging it is possible to output all reads (-a/–all-reads) which will re-create the input BAM with the addition of tags on matching reads.
The default set of sequences include a range of different Illumina adapter sequences with the sample index/barcode region masked to Ns.
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| input | i | PathToBam | Input SAM or BAM file | Required | 1 | |
| output | o | PathToBam | Output SAM or BAM file | Required | 1 | |
| match-length | m | Int | The number of bases at the start of the read to match against. | Optional | 1 | 15 |
| max-errors | e | Int | The maximum number of errors in the matched region. | Optional | 1 | 1 |
| sequences | s | String | The set of technical sequences to look for. | Required | Unlimited | AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCTGAGCGGGCTGGCAAGGCAGACCGNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG |
| all-reads | a | Boolean | Output all reads. | Optional | 1 | false |
| tag | t | String | Tag to set to indicate a read is a technical sequence. | Optional | 1 |