Repositories list

• quicksand

  Public
  A pipeline for the analysis of sedimentary ancient mtDNA

  dockerbioinformaticspipeline+ 4nextflowsingularityancient-dnasedadna

  Nextflow

  •

  MIT License

  •2•5•3•0•Updated Nov 14, 2024Nov 14, 2024

• mapAD

  Public
  An aDNA aware short-read mapper

  Rust

  •

  MIT License

  •0•19•0•0•Updated Nov 12, 2024Nov 12, 2024

• quicksand-build

  Public
  The mpieva/quicksand helper pipeline

  bioinformaticspipeline

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

• network-aware-bwa

  Public
  the Burrows Wheeler Aligner with networking capabilities

  C

  •

  GNU General Public License v3.0

  •3•5•0•1•Updated Jun 8, 2022Jun 8, 2022

• biohazard

  Public
  Udo Stenzel's biohazard — a Haskell library for bioinformatics [MIRROR]

  haskell-libraryhaskellbioinformatics+ 1cabal

  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 sequencing.

  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]

  haskellbioinformaticscommand-line+ 2bam-filescabal

  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

  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

  •23k•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+ 6ngsnext-generation-sequencingbamilluminabcldemultiplexing

  Haskell

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated May 15, 2019May 15, 2019

• BCL2BAM2FASTQ

  Public
  C++

  •3•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+ 3rstatsbioconductoradmixture

  R

  •

  Other

  •9•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-filesngsnext-generation-sequencing+ 7phylogeneticsperl5bamsamtoolsphylogenyperlbed

  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+ 2variationvcf

  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+ 2ontologygene-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

  •1•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

  bioinformaticsgenomicsmitochondria+ 3alignmentcontaminationconsensus-calling

  C

  •

  Artistic License 2.0

  •7•16•3•0•Updated Jul 29, 2013Jul 29, 2013