Implement read mapping action - Githubissues

bokulich-lab / q2-assembly

QIIME 2 plugin for (meta)genome assembly.

BSD 3-Clause "New" or "Revised" License

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Implement read mapping action #5

Closed misialq closed 2 years ago

misialq commented 3 years ago

We need an action supporting mapping reads to indexed contigs/MAGs using bowtie2.

Acceptance criteria:

uses SampleData[*SequencesWithQuality] and SampleData[MultiBowtie2Index | Bowtie2Index]
uses bowtie2 to align reads
outputs SampleData[AlignmentMaps | AlignmentMap]

Notes:

perhaps this needs to be split into two actions: one for single- and one for paired-end reads...? (perhaps not)