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About me

I'm a bioinformatician with a computational biology PhD from ETH Zürich. Employed as full-time remote Principal Software Engineer and Associate Director Bioinformatics at PacBio since 2014 and responsible for most of PacBio's analysis tools. My day-to-day business is working on sequence analysis algorithms using hardware-near C++, designing software architectures, tech-leading, and Agile stuff. You can get my attention if you work on specialized bioinformatics algorithms, software architectures, or bare metal.

You can find more info on ArminToepfer.com, LinkedIn, or Twitter.

Get my public key curl https://keybase.io/armintoepfer/pgp_keys.asc | gpg --import

PacBio Tool Highlights

PhD Tool Highlights

Armin Töpfer's Projects

bamextract icon bamextract

Extracts regions from a bam file and exports as in sam format

genomeworks icon genomeworks

SDK for GPU accelerated genome assembly and analysis

ggeyecandy icon ggeyecandy

Various R scripts to generate appealing data visualizations

haploclique icon haploclique

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.

just-the-docs icon just-the-docs

A modern, high customizable, responsive Jekyll theme for documention with built-in search.

oligomatcher icon oligomatcher

OligoMatcher finds all genes, which are target of an oligo.

profilesim icon profilesim

Creating profiles for SimSeq from BAM alignments and a set of reference genomes.

samtools icon samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

seqalfixer icon seqalfixer

SequenceAlignmentFixer, a multitude of alignment statistics and fixes for Next Generation Sequencing (NGS) data. Computes consensus sequence with in-frame deletions and insertions.

split2del icon split2del

Bioinformatics tool to merge split read alignments to reconstruct large deletions.

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