https://github.com/ssi-dk/bifrost_assemblatron

Bifrost Component: Assemblatron - De-novo assembly of paired reads for QC and downstream Analysis purposes
https://github.com/ssi-dk/bifrost_assemblatron

Last synced: 3 days ago
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Bifrost Component: Assemblatron - De-novo assembly of paired reads for QC and downstream Analysis purposes

• Host: GitHub
• URL: https://github.com/ssi-dk/bifrost_assemblatron
• Owner: ssi-dk
• License: mit
• Created: 2019-10-18T08:28:21.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2023-11-06T09:54:11.000Z (about 1 year ago)
• Last Synced: 2023-11-06T10:34:50.562Z (about 1 year ago)
• Language: Python
• Size: 113 KB
• Stars: 0
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: HISTORY.md
  • License: LICENSE

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README

        
# bifrost_assemblatron

This component is run given a sample id already added into the bifrostDB. From this it'll pull the paired_reads and contigs and remap the raw reads to the assembly. From the resulting files various QC metrics will be captured.

## Programs: (see Dockerfile) 

```

snakemake-minimal==5.31.1;

bbmap==38.58;

skesa==2.4.0;

```

## Summary of c run: (see pipeline.smk and config.yaml)

```

java -ea -cp /opt/conda/opt/bbmap-38.58-0/current/ jgi.BBDuk in={input.reads[0]} in2={input.reads[1]} out={output.filtered_reads} ref={params.adapters} ktrim=r k=23 mink=11 hdist=1 tbo qtrim=r minlength=30 1> {log.out_file} 2> {log.err_file}

skesa --use_paired_ends --fastq {input.filtered_reads} --contigs_out {output.contigs} 1> {log.out_file} 2> {log.err_file}

```