https://github.com/dfornika/kma-match-ref
Use the kma aligner to choose the best reference from a multi-fasta database
https://github.com/dfornika/kma-match-ref
Last synced: 3 months ago
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Use the kma aligner to choose the best reference from a multi-fasta database
- Host: GitHub
- URL: https://github.com/dfornika/kma-match-ref
- Owner: dfornika
- Created: 2022-05-03T20:14:00.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2022-05-09T22:35:29.000Z (about 3 years ago)
- Last Synced: 2025-01-24T23:48:49.210Z (4 months ago)
- Language: Python
- Size: 8.79 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# KMA Match Reference
This pipeline uses the [kma](https://bitbucket.org/genomicepidemiology/kma) aligner to align raw sequence data against
a database of similar reference genomes, and choose the one that best matches the input sequence data. Choice of best
reference sequence is made based on the Q score provided by kma for each reference.
For more details on kma parameters and outputs, see the [kma specification](https://bitbucket.org/genomicepidemiology/kma/raw/8dd45bf6e8e92eb143865433b09ef7b572f8762c/KMAspecification.pdf)
## Usage
```
nextflow run dfornika/kma-match-ref \
--fastq_input \
--ref_db \
--outdir
```
## Outputs
```
.
├── sample-01.bam
├── sample-01.bam.bai
├── sample-01_bamqc
│ ├── css
│ ├── genome_results.txt
│ ├── images_qualimapReport
│ ├── qualimapReport.html
│ └── raw_data_qualimapReport
├── sample-01_depth_by_position.tsv
├── sample-01_fastp.csv
├── sample-01_fastp.json
├── sample-01_kma.csv
├── sample-01_qualimap_bamqc_genome_results.csv
└── sample-01_ref.fa
```