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@mpieva MPI EVA Bioinformatics

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    29 repositories

    • mapAD

      Public
      An aDNA aware short-read mapper
      Rust
      •
      MIT License
      •0•22•0•0•Updated Apr 22, 2026Apr 22, 2026

    • postprocessing

      Public
      Basic post-processing for human shotgun and nuclear capture libraries
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • NED-flow

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • quicksand

      Public
      A pipeline for the analysis of sedimentary ancient mtDNA.
      dockerbioinformaticspipeline
      dockerbioinformaticspipelinenextflowsingularityancient-dnasedadna
      Nextflow
      •
      MIT License
      •3•15•4•0•Updated Feb 9, 2026Feb 9, 2026

    • quicksand-build

      Public
      The mpieva/quicksand helper pipeline
      bioinformaticspipeline
      bioinformaticspipeline
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • network-aware-bwa

      Public
      the Burrows Wheeler Aligner with networking capabilities
      C
      •
      GNU General Public License v3.0
      •4•6•0•2•Updated Jun 8, 2022Jun 8, 2022

    • biohazard

      Public
      Udo Stenzel's biohazard — a Haskell library for bioinformatics [MIRROR]
      haskellbioinformaticshaskell-library
      haskellbioinformaticshaskell-librarycabal
      Haskell
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 5, 2022Apr 5, 2022

    • index_swapping

      Public
      Perl script for identifying cross-contamination events that occurred between double-index libraries due to index swapping during library amplification or sequen…
      bioinformatics
      bioinformatics
      Perl
      •
      MIT License
      •0•0•0•0•Updated Nov 5, 2021Nov 5, 2021

    • biohazard-tools

      Public
      Udo Stenzel's biohazard-tools — a collection of command-line utilities for bioinformatics [MIRROR]
      haskellbam-filesbioinformatics
      haskellbam-filesbioinformaticscommand-linecabal
      Haskell
      •
      BSD 3-Clause "New" or "Revised" License
      •1•7•0•0•Updated Mar 18, 2021Mar 18, 2021

    • nuclear_sediment_pipeline

      Public
      Scripts used within the sediment capture pipeline
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 26, 2021Jan 26, 2021

    • matchseq

      Public
      Perl scripts for reconstructing the structure of double-stranded DNA fragments from single-stranded DNA libraries
      bioinformaticsgenomicsancientdna
      bioinformaticsgenomicsancientdna
      Perl
      •
      MIT License
      •1•2•0•0•Updated May 15, 2020May 15, 2020

    • swot

      Public
      Identify email addresses or domains names that belong to colleges or universities. Help automate the process of approving or rejecting academic discounts.
      Kotlin
      •
      MIT License
      •37k•0•0•0•Updated Apr 15, 2020Apr 15, 2020

    • GOfuncR

      Public
      R-package for GO-enrichment analyses
      C++
      •6•0•0•0•Updated Apr 5, 2020Apr 5, 2020

    • SpAl

      Public
      Estimating Spurious Alignments in ancient DNA
      Python
      •0•0•0•0•Updated Dec 6, 2019Dec 6, 2019

    • jivebunny

      Public
      Udo Stenzel’s jivebunny — a probabilistic demultiplexer for Illumina sequencing data [MIRROR]
      haskellbam-filesbioinformatics
      haskellbam-filesbioinformaticsngsnext-generation-sequencingbamilluminabcldemultiplexing
      Haskell
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated May 15, 2019May 15, 2019

    • BCL2BAM2FASTQ

      Public
      C++
      •2•0•0•0•Updated Feb 6, 2019Feb 6, 2019

    • deML

      Public
      Maximum likelihood demultiplexing
      C++
      •
      GNU General Public License v3.0
      •14•0•0•0•Updated Feb 6, 2019Feb 6, 2019

    • admixr

      Public
      An R package for running ADMIXTOOLS analyses directly within R. See the project website at https://bodkan.net/admixr.
      bioinformaticsrgenomics
      bioinformaticsrgenomicsrstatsbioconductoradmixture
      R
      •
      Other
      •10•0•0•0•Updated Jan 16, 2019Jan 16, 2019

    • libgab

      Public
      A C++ class of useful little functions
      C++
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Jul 13, 2018Jul 13, 2018

    • perl-ngs

      Public
      Udo Stenzel's perl-ngs — a collection of Perl tools for next-generation sequencing [MIRROR]
      bam-filesperlngs
      bam-filesperlngsnext-generation-sequencingphylogeneticsperl5bedbamsamtoolsphylogeny
      Perl
      •
      MIT License
      •0•0•0•0•Updated Feb 28, 2018Feb 28, 2018

    • aLib

      Public
      Python
      •2•0•0•0•Updated Feb 28, 2018Feb 28, 2018

    • heffalump

      Public
      Udo Stenzel’s Heffalump — a file format that stores genetic variation and the tool to work with it [MIRROR]
      haskellbioinformaticsgenomics
      haskellbioinformaticsgenomicsvcfvariation
      Haskell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 28, 2018Feb 28, 2018

    • schmutzi

      Public
      Maximum a posteriori estimate of contamination for ancient samples
      C++
      •2•0•0•0•Updated Jan 26, 2018Jan 26, 2018

    • func

      Public
      Kay Prüfer’s FUNC — a package for detecting significant associations between gene sets and ontological annotations
      bioinformaticsgenomicsgenetics
      bioinformaticsgenomicsgeneticsontologygene-ontology
      C++
      •
      GNU General Public License v2.0
      •1•0•0•0•Updated Jan 9, 2018Jan 9, 2018

    • leeHom

      Public
      Bayesian reconstruction of ancient DNA fragments
      C++
      •
      GNU General Public License v3.0
      •14•0•0•0•Updated Dec 8, 2017Dec 8, 2017

    • samtools-patched

      Public
      an old copy of samtools (from samtools.sf.net) with lots of patches
      C
      •
      MIT License
      •0•1•0•0•Updated Sep 22, 2016Sep 22, 2016

    • freeIbis

      Public
      An efficient basecaller for Illumina sequencers with calibrated quality scores
      Python
      •4•0•0•0•Updated Jul 24, 2015Jul 24, 2015

    • anfo

      Public
      The ANFO ancient DNA mapper
      C++
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Jul 7, 2014Jul 7, 2014

    • mapping-iterative-assembler

      Public
      Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria
      bioinformaticsgenomicsalignment
      bioinformaticsgenomicsalignmentcontaminationmitochondriaconsensus-calling
      C
      •
      Artistic License 2.0
      •7•19•4•0•Updated Jul 29, 2013Jul 29, 2013
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