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how to get aligned.bam from wtdbg2 for quiver?

Hi, I am new to Pacbio sequence (sequel) analysis. I am trying to do a denovo assembly for a test data set (used subreads.fastq). I managed to construct an assembly using wtdbg2. I also ran wtdbg-cns to get consensus assembly, consensus.fa (*.lay.gz as input). However, I completely lost the way when I started to use quiver. It needs an aligned bam file. I am not sure how to get that from wtdbg2. any idea how to get that? thanks in advance Shri

assembly
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updated by h.mon h.mon • written by shripathiacademics • shripathiacademics

wtdbg2 is an assembler. You will need to use an aligner to get the aligned BAM file from your original data. @h.mon has recommendations for that below.

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written by GenoMax GenoMax

1 answer

Use minimap2, or PacBio front-end to it, pbmm2.

edit: by the way, Quiver is the legacy consensus builder from PacBio, Arrow is the currently maintained tool. In addition, I would suggest Racon as a good first alternative.

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written by h.mon h.mon

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