0.6.0-bwa

polypolish container

Main tool: polypolish v0.6.0

Code repository: polypolish

Additional tools:

• bwa: 0.7.18
• python: 3.10

Basic information on how to use this tool:

• executable: polypolish
• help: --help
• version: --version
• description: "Polypolish "polishes" consensus files created during assembly of long reads with Illumina short reads. Polypolish is a little different than other polishing tools in that paired-end reads need to be aligned separatly to generate two sam files."

Additional information: This container also includes BWA v0.7.18 so that the user can align their short reads within the same container.

Full documentation: https://github.com/rrwick/Polypolish/wiki

Example Usage

Use the included bwa software to align reads to the draft sequence. Please note that bbamp, minimap2 or any other similar software can perform a similar step that may be better suited for your use-case.

bwa index draft.fasta
bwa mem -t 16 -a draft.fasta reads_1.fastq.gz > alignments_1.sam
bwa mem -t 16 -a draft.fasta reads_2.fastq.gz > alignments_2.sam

Once the sam files are generated, they can be used with polypolish.

# paired end
polypolish filter --in1 alignments_1.sam --in2 alignments_2.sam --out1 filtered_1.sam --out2 filtered_2.sam
polypolish polish draft.fasta filtered_1.sam filtered_2.sam > polished.fasta

# single end
polypolish polish draft.fasta input.sam > polished.fasta