jonas-fuchs / bamdash

create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks

Welcome 🦊

I am currently working as a Post-Doc at the Institute for Virology in Freiburg leading the in-house NGS sequencing laboratory. We focus on viral genomics and intra-host evolution of diverse pathogens (Hepatitis E virus, SARS-CoV-2, Influenza A, MPXV and HSV-1). I started bioinformatics at the beginning of the SARS-CoV-2 pandemic and have been in love with big data, genomics, metagenomics, coding and pyhlogenetics ever since. I am a super weird mixture of wet-lab molecular virologist, bioinformatician, data scientist, NGS specialist, epidemiologist, clinical scientist and nerd.

Skills ✔️

Software 💾

I am working on software for viral genomics. Available through pip and conda.

• BAMdash Aggregate your virus sequencing results into an interactive plot.
• varVAMP Design primers for PCR on highly variable alignments.
• virHEAT Compare vcf files as a heatmap.

Publications 📜

• Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient as a source of immune escape variants

• Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient

• Antibody escape and global spread of SARS-CoV-2 lineage A. 27

• Evolution and antiviral specificities of interferon-induced Mx proteins of bats against Ebola, influenza, and other RNA viruses

• The landscape of SARS-CoV-2 RNA modifications

• Comparative Study of Ten Thogotovirus Isolates and Their Distinct In Vivo Characteristics

• Tick-transmitted thogotovirus gains high virulence by a single MxA escape mutation in the viral nucleoprotein

• Case series: convalescent plasma therapy for patients with COVID-19 and primary antibody deficiency

  ... Full list of publications

bamdash's Issues

Run BAMdash on multiple reference contigs

Is this possible?

For example, imagine a segmented virus. And I want to get the coverage for all segments.

Do I have to run the tool multiple times for each contig ID. Or might it be possible to run that automatically and have a drop down menu to select the different contigs in the visual?

The example it's not working

I tried the command, but I'm getting this error:

bamdash -b HEV.bam -r HEV-pat-1 -t HEV.vcf HEVprim.bed HEVamp.bed HEV.gb
[W::vcf_parse] Contig 'HEV-pat-1' is not defined in the header. (Quick workaround: index the file with tabix.)

Another question is related to the running time. I was plotting a specific virus coverage using only the bed info in the -t command. Is it normal to take more than one day to run? I tried the "--export_static" with pdf. Could this be slowing the process?

Plot does not show any coverage

Hey!

I am maybe misusing the tool but I have a small FASTA file that I mapped to a SC2 reference and then I wanted to visualize. Attached is the sorted BAM file after mapping with minimap2.

Then I used

samtools index baits.sorted.bam
bamdash -b baits.sorted.bam -r NC_045512.2

which works without error. But the plot looks like this:

What am I missing?

Thx!

baits.sorted.bam.gz