how to get aligned.bam from wtdbg2 for quiver?

Question

[shripathiacademics]

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

[GenoMax]

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.

Answer 1

[h.mon]

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.