pmenzel

Bioinformatics Scientist at @LaborBerlin, prev at MDC Berlin, KU.dk, Uni Leipzig

@LaborBerlin Berlin

Pinned Repositories

kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Language:C259 14 26668
biq
Tool for indexing and querying back-splice junctions of circular RNAs (circRNAs) in RNA-Seq datasets
Language:JavaScript3 2 00
download-refseq-genomes
Perl script to download genomes within a clade from NCBI Refseq
Language:Perl5 3 41
gh-actions
workflows for GitHub Actions
Language:Perl5 2 10
kiq
K-mer indexing and querying in RNA-Seq data
Language:C++6 3 10
ont-assembly-snake
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools
Language:Python18 4 162
packCircles
C program for space-efficiently packing circles in a plane.
Language:C17 5 11
plot-samtools-depth
Plot output of samtools depth to postscript
Language:C3 1 20
score-assemblies
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
Language:Python24 3 101
taxonomy-tools
C++ tools for NCBI taxonomy tasks
Language:C++11 2 03

pmenzel's Repositories

pmenzel/score-assemblies
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
Language:Python24 3 101
pmenzel/ont-assembly-snake
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools
Language:Python18 4 162
pmenzel/packCircles
C program for space-efficiently packing circles in a plane.
Language:C17 5 11
pmenzel/taxonomy-tools
C++ tools for NCBI taxonomy tasks
Language:C++11 2 03
pmenzel/download-refseq-genomes
Perl script to download genomes within a clade from NCBI Refseq
Language:Perl5 3 41
pmenzel/gh-actions
workflows for GitHub Actions
Language:Perl5 2 10
pmenzel/plot-samtools-depth
Plot output of samtools depth to postscript
Language:C3 1 20
pmenzel/raconnn
wrapper for running multiple assembly polishing rounds with racon
Language:Shell2 2 0
pmenzel/sarscov2-analysis-resources
2 2 0
pmenzel/illumina-assembly-snake
Snakemake wrapper for bacterial genome assembly from Illumina reads.
Language:Python1 1 1
pmenzel/Recipes
1 2 0
pmenzel/advent-of-code
Language:Perl2 0
pmenzel/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell1 0
pmenzel/deeperseq
Browse FASTQs for SARS-CoV-2 genomes from the SRA/ENA
Language:JavaScript1 0
pmenzel/dht22-rpi
Language:Python1 0
pmenzel/dircolors-solarized
This is a repository of themes for GNU ls (configured via GNU dircolors) that support Ethan Schoonover’s Solarized color scheme.
Language:Makefile1 0
pmenzel/docker-backuppc
Docker container with BackupPC version 4.x/3.x based on Alpine distribution.
Language:Shell1 0
pmenzel/docker-micromamba-shiny
A minimal example for an R Shiny app inside a Docker container using R packages via conda-forge + micromamba
Language:R2 0
pmenzel/download-genbank-genomes
Language:Perl2 0
pmenzel/Filtlong
quality filtering tool for long reads
Language:C++1 0
pmenzel/kaiju-testdata
2 0
pmenzel/LS_COLORS
A collection of LS_COLORS definitions; needs your contribution!
Language:Shell1 0
pmenzel/ont-assembly-snake-testdata
pmenzel/open-data-registry
A registry of publicly available datasets on AWS
Language:Python
pmenzel/pmenzel
2 0
pmenzel/r-ggstatsplot-feedstock
A conda-smithy repository for r-ggstatsplot.
Language:Shell1 0
pmenzel/sarscov2-inzidenzen
Language:R2 0
pmenzel/stable-diffusion
Language:Jupyter Notebook1 0
pmenzel/tapiriik
tapiriik keeps your fitness in sync
Language:Python2 0
pmenzel/TBProfiler
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
Language:Python1 0