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# Yanosim (yet another nanopore simulator)
Read simulator for nanopore DRS datasets.
## Installation:
`pip install git+git://github.com/bartongroup/yanosim`
## Usage:
### `model`:
```
$ yanosim model --help
Usage: yanosim model [OPTIONS]
Creates an model of mismatches, insertions and deletions based on an
alignment of nanopore DRS reads to a reference. Reads should be aligned to
a transcriptome i.e. without spliced alignment, using minimap2. They
should have the cs tag.
Options:
-b, --bam-fn TEXT [required]
-o, --output-fn TEXT [required]
-p, --processes INTEGER
--help Show this message and exit.
```
### `quantify`:
```
$ yanosim quantify --help
Usage: yanosim quantify [OPTIONS]
Quantify the number of reads mapping to each transcript in a reference, so
that the right number of reads can be simulated.
Options:
-b, --bam-fn TEXT [required]
-o, --output-fn TEXT [required]
-g, --gtf-fn TEXT
-f, --filtered-gtf-output-fn TEXT
-r, --remove-ensembl-version
--help Show this message and exit.
```
### `simulate`:
```
$ yanosim simulate --help
Usage: yanosim simulate [OPTIONS]
Given a model created using yanosim model, and per-transcript read counts
created using yanosim simulate, simulate error-prone long-reads from the
given fasta file.
Options:
-f, --fasta-fn TEXT [required]
-m, --model-fn TEXT [required]
-q, --quantification-fn TEXT [required]
-o, --output-fn TEXT [required]
--model-frag / --no-model-frag
-p, --processes INTEGER
-s, --seed INTEGER
--help Show this message and exit.
```
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