Tools for working with genomic and high throughput sequencing data.
Group: Utilities
Picks a set of molecular indices that should work well together.
The indexes to evaluate are generated randomly, unless the --candidates option is given. The latter
specifies a path to a file with one index per line from which indices are picked.
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| length | l | Int | The length of each barcode sequence. | Optional | 1 | 8 |
| indices | n | Int | The number of indices desired. | Required | 1 | |
| edit-distance | e | Int | The minimum edit distance between two indices in the set. | Optional | 1 | 3 |
| output | o | FilePath | File to write indices to. | Required | 1 | |
| allow-reverses | Boolean | Allow indices that are lexical reverses of one another | Optional | 1 | false | |
| allow-reverse-complements | Boolean | Allow indices that are reverse complements of one another | Optional | 1 | false | |
| allow-palindromes | Boolean | Allow indices that are palindromic (bases == rev(bases)). |
Optional | 1 | false | |
| max-homopolymer | Int | Reject indices with a homopolymer of greater than this length. | Optional | 1 | 2 | |
| min-gc | Double | The minimum GC fraction for a barcode to be accepted. | Optional | 1 | 0.0 | |
| max-gc | Double | The maximum GC fraction for a barcode to be accepted. | Optional | 1 | 0.7 | |
| threads | t | Int | Number of threads to use. | Optional | 1 | 4 |
| vienna-rna-dir | DirPath | The installation directory for ViennaRNA. |
Optional | 1 | ||
| min-delta-g | Double | The lowest acceptable secondary structure deltaG. |
Optional | 1 | -10.0 | |
| adapters | String | The indexed adapter sequence into which the indices will be integrated. | Required | Unlimited | AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG | |
| avoid-sequence | String | Sequences that should be avoided. Any kmer of length that appears in these sequences and their reverse complements will be thrown out. |
Required | Unlimited | AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCTGAGCGGGCTGGCAAGGCAGACCGNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG | |
| candidates | FilePath | The candidate indices from which to choose with one index per line (nothing else), otherwise generate all possible indices | Optional | 1 |