jonas-fuchs/varvamp

Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.

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

varvamp's Issues

Problem combining qpcr mode with primer blast

when trying to combine mode qpcr with -db I'm running into:

Traceback (most recent call last):
  File "/home/wolma/miniconda3/envs/varvamp/bin/varvamp", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/wolma/miniconda3/envs/varvamp/lib/python3.11/site-packages/varvamp/command.py", line 554, in main
    probe_regions, final_schemes = qpcr_workflow(
                                   ^^^^^^^^^^^^^^
  File "/home/wolma/miniconda3/envs/varvamp/lib/python3.11/site-packages/varvamp/command.py", line 450, in qpcr_workflow
    query_path = blast.create_BLAST_query_qpcr(qpcr_scheme_candidates, data_dir)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/wolma/miniconda3/envs/varvamp/lib/python3.11/site-packages/varvamp/scripts/blast.py", line 62, in create_BLAST_query_qpcr
    name = f"{primer_type}_{qpcr_scheme_candidates[amp][primer_type][1]}_{qpcr_scheme_candidates[amp][primer_type][2]}"

KeyError: 'probe'

which, at first glance, looks like a rather generic error that wouldn't depend on exact inputs, but let me know if you need more details to reproduce this.

Combination of qPCR and BLAST db fails

  File "/usr/local/tools/_conda/envs/mulled-v1-88ec11123572a51b245ba097dc0b273940132dc7e25597f386c2d705a3f21960/bin/varvamp", line 10, in <module>
    sys.exit(main())
  File "/usr/local/tools/_conda/envs/mulled-v1-88ec11123572a51b245ba097dc0b273940132dc7e25597f386c2d705a3f21960/lib/python3.10/site-packages/varvamp/command.py", line 557, in main
    probe_regions, final_schemes = qpcr_workflow(
  File "/usr/local/tools/_conda/envs/mulled-v1-88ec11123572a51b245ba097dc0b273940132dc7e25597f386c2d705a3f21960/lib/python3.10/site-packages/varvamp/command.py", line 455, in qpcr_workflow
    amplicons, off_target_amplicons = blast.primer_blast(
  File "/usr/local/tools/_conda/envs/mulled-v1-88ec11123572a51b245ba097dc0b273940132dc7e25597f386c2d705a3f21960/lib/python3.10/site-packages/varvamp/scripts/blast.py", line 240, in primer_blast
    off_target_amplicons, amplicons = predict_non_specific_amplicons(
  File "/usr/local/tools/_conda/envs/mulled-v1-88ec11123572a51b245ba097dc0b273940132dc7e25597f386c2d705a3f21960/lib/python3.10/site-packages/varvamp/scripts/blast.py", line 206, in predict_non_specific_amplicons
    amplicons[off_target]["penalty"][0] = amplicons[off_target]["penalty"][0] + config.BLAST_PENALTY
TypeError: 'float' object is not subscriptable```

Warning about deprecated Biopython functionality

With recent enough versions of Biopython varVAMP triggers the deprecation warning from:

https://github.com/biopython/biopython/blob/4fc5158970b7970907fb932eae15eb779fdea839/Bio/Application/__init__.py#L40-L49

varVAMP should do as suggested in the warning and call blast directly via stdlib subprocess.

Error response from daemon

$ docker pull quay.io/biocontainers/varvamp
Using default tag: latest
Error response from daemon: manifest for quay.io/biocontainers/varvamp:latest not found: manifest unknown: manifest unknown

could you tell me How fix it?

END_OVERLAP config setting not getting logged

config.END_OVERLAP is a setting that does not get echoed to the log file.
I'm also wondering whether it got placed into the qPCR section of settings in the default config by accident because the code appears to use it for regular primers, too.

threshold for conserved nucleotides

Can you explain it in more detail?
-t 0.89, --threshold 0.89 threshold for conserved nucleotides

Which of the following is more similar in meaning?

1. 89% nucleotides in probe and primers are conserved in all genomes;

2. or, >89% nucleotides other than primers and probes are conserved in amplicon;
3. or, >89% of all genomes maybe be amplified