mpieva/quicksand

A pipeline for the analysis of sedimentary ancient mtDNA

Language: Nextflow - Size: 131 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 4 - Forks: 0

mpieva/mapAD

An aDNA aware short-read mapper

Language: Rust - Size: 11.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 19 - Forks: 0

mpieva/quicksand-build

The mpieva/quicksand helper pipeline

Language: Nextflow - Size: 75.2 KB - Last synced: about 2 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

mpieva/libgab Fork of grenaud/libgab

A C++ class of useful little functions

Language: C++ - Size: 106 KB - Last synced: about 2 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

mpieva/heffalump

Udo Stenzel’s Heffalump — a file format that stores genetic variation and the tool to work with it [MIRROR]

Language: Haskell - Size: 320 KB - Last synced: about 2 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

mpieva/aLib Fork of grenaud/aLib

Language: Python - Size: 23.1 MB - Last synced: about 2 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

mpieva/anfo

The ANFO ancient DNA mapper

Language: C++ - Size: 1.97 MB - Last synced: about 2 months ago - Pushed: almost 10 years ago - Stars: 0 - Forks: 0

mpieva/swot Fork of JetBrains/swot

Identify email addresses or domains names that belong to colleges or universities. Help automate the process of approving or rejecting academic discounts.

Size: 19.8 MB - Last synced: about 2 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

mpieva/schmutzi Fork of grenaud/schmutzi

Maximum a posteriori estimate of contamination for ancient samples

Language: C++ - Size: 41.9 MB - Last synced: about 2 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

mpieva/SpAl

Estimating Spurious Alignments in ancient DNA

Size: 12.7 KB - Last synced: about 2 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

mpieva/admixr Fork of bodkan/admixr

An R package for running ADMIXTOOLS analyses directly within R. See the project website at https://bodkan.net/admixr.

Language: R - Size: 8.39 MB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

mpieva/index_swapping

Perl script for identifying cross-contamination events that occurred between double-index libraries due to index swapping during library amplification or sequencing.

Language: Perl - Size: 1.39 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

mpieva/deML Fork of grenaud/deML

Maximum likelihood demultiplexing

Language: C++ - Size: 23 MB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

mpieva/BCL2BAM2FASTQ Fork of grenaud/BCL2BAM2FASTQ

Language: C++ - Size: 31.3 KB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

mpieva/GOfuncR Fork of sgrote/GOfuncR

R-package for GO-enrichment analyses

Size: 135 MB - Last synced: about 2 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

mpieva/leeHom Fork of grenaud/leeHom

Bayesian reconstruction of ancient DNA fragments

Language: C++ - Size: 18.1 MB - Last synced: about 2 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

mpieva/biohazard

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

Language: Haskell - Size: 1.46 MB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

mpieva/mapping-iterative-assembler

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Language: C - Size: 572 KB - Last synced: about 2 months ago - Pushed: almost 11 years ago - Stars: 15 - Forks: 7

mpieva/samtools-patched

an old copy of samtools (from samtools.sf.net) with lots of patches

Language: C - Size: 487 KB - Last synced: about 2 months ago - Pushed: over 7 years ago - Stars: 1 - Forks: 1

mpieva/func

Kay Prüfer’s FUNC — a package for detecting significant associations between gene sets and ontological annotations

Language: C++ - Size: 113 KB - Last synced: about 2 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 1

mpieva/perl-ngs

Udo Stenzel's perl-ngs — a collection of Perl tools for next-generation sequencing [MIRROR]

Language: Perl - Size: 16.6 KB - Last synced: about 2 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

mpieva/matchseq

Perl scripts for reconstructing the structure of double-stranded DNA fragments from single-stranded DNA libraries

Language: Perl - Size: 21.5 KB - Last synced: about 2 months ago - Pushed: about 4 years ago - Stars: 2 - Forks: 0

mpieva/biohazard-tools

Udo Stenzel's biohazard-tools — a collection of command-line utilities for bioinformatics [MIRROR]

Language: Haskell - Size: 149 KB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 7 - Forks: 0

mpieva/network-aware-bwa

the Burrows Wheeler Aligner with networking capabilities

Language: C - Size: 655 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 5 - Forks: 3

mpieva/nuclear_sediment_pipeline

Scripts used within the sediment capture pipeline

Language: Python - Size: 20.3 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

mpieva/jivebunny

Udo Stenzel’s jivebunny — a probabilistic demultiplexer for Illumina sequencing data [MIRROR]

Language: Haskell - Size: 82 KB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 1

mpieva/freeIbis Fork of grenaud/freeIbis

An efficient basecaller for Illumina sequencers with calibrated quality scores

Language: Python - Size: 4.01 MB - Last synced: about 2 months ago - Pushed: almost 9 years ago - Stars: 0 - Forks: 0