armintoepfer
Husband. Father. Computational biology PhD. Bioinformagician. Principal Software Engineer & Associate Director. C++ Purist. Geek. Digital Artist. Photographer.
@PacificBiosciences Gelsenkirchen
Pinned Repositories
bam-io-throughput
BAM I/O Throughput Benchmark
fastpool
ggeyecandy
Various R scripts to generate appealing data visualizations
haploclique
Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
barcoding
Lima - Demultiplex Barcoded PacBio Samples
ccs
CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
IsoSeq
Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
minorseq
Minor Variant Calling and Phasing Tools
pbbioconda
PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
pbsv
pbsv - PacBio structural variant (SV) calling and analysis tools
armintoepfer's Repositories
armintoepfer/haploclique
Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
armintoepfer/bam-io-throughput
BAM I/O Throughput Benchmark
armintoepfer/fastpool
armintoepfer/ggeyecandy
Various R scripts to generate appealing data visualizations
armintoepfer/aligner-testbed
armintoepfer/BAMExtract
Extracts regions from a bam file and exports as in sam format
armintoepfer/PrimerIDTK
Toolkit for PrimerID NGS experiments
armintoepfer/profilesim
Creating profiles for SimSeq from BAM alignments and a set of reference genomes.
armintoepfer/QuasiViz
Visualisation of viral populations
armintoepfer/seqalfixer
SequenceAlignmentFixer, a multitude of alignment statistics and fixes for Next Generation Sequencing (NGS) data. Computes consensus sequence with in-frame deletions and insertions.
armintoepfer/split2del
Bioinformatics tool to merge split read alignments to reconstruct large deletions.
armintoepfer/armintoepfer
armintoepfer/GenomeWorks
SDK for GPU accelerated genome assembly and analysis
armintoepfer/just-the-docs
A modern, high customizable, responsive Jekyll theme for documention with built-in search.
armintoepfer/OligoMatcher
OligoMatcher finds all genes, which are target of an oligo.
armintoepfer/samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data