https://github.com/jts/assembly_accuracy
tools for assessing the accuracy of genome assemblies
https://github.com/jts/assembly_accuracy
Last synced: 5 months ago
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tools for assessing the accuracy of genome assemblies
- Host: GitHub
- URL: https://github.com/jts/assembly_accuracy
- Owner: jts
- License: mit
- Created: 2018-08-15T15:36:27.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2024-04-16T02:47:08.000Z (about 2 years ago)
- Last Synced: 2024-04-16T03:49:45.242Z (about 2 years ago)
- Language: Python
- Size: 8.79 KB
- Stars: 34
- Watchers: 4
- Forks: 4
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Tools for assessing the accuracy of a genome assembly
This repository contains a small tool to assess the accuracy of an assembly using minimap2.
It requires the `pyvcf` and `pysam` python packages, and `minimap2` to be on your PATH.
## Usage
```
fastmer.py --reference reference.fasta --assembly assembly.fasta --min-mapping-quality 10
```
## Example output:
```
assembly_name percent_identity qscore num_matches num_mismatches num_insertions num_deletions 4mer_acc 5mer_acc 6mer_acc 7mer_acc 8mer_acc 9mer_acc
nanopolish_r94 99.956154 33.58 4691618 163 730 1165 0.995 0.983 0.923 0.825 0.730 0.545
```