Tool to Create Sequence Logo Plot with Indels or Alignment-Aware Position Frequency Matrix

Question

[Charles-Alexandre Roy]

Given an alignment file (e.g. SAM, BAM), has anyone come across a tool that can create the equivalent of a sequence logo plot that also includes indels? Or, similarly, a tool to generate a position frequency matrix that includes indels?

My goal is to illustrate how a set of reads relates to the reference genome in aggregate over a given region.

I'm imagining a hybrid of Samtools Tview (e.g. below) and sequence logo plots such that insertions and deletions in multiple reads are collapsed and represented by frequency.

[Jeremy Leipzig]

you could combine a sequence logo with a splice graph but there's nothing about either of them that allows you to relate neighboring positions with each other

Answer 1

[Mensur Dlakic]

Most logo programs work without displaying indels. However, it may work if you can extract the alignment from this region and make a hidden Markov model (HMM) from it. There are tools to model indels in HMMs.

• https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-5-7
• https://www.sanger.ac.uk/tool/logomat-m/
• https://skylign.org/