grenaud/mappability_snpable

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Created over 2 years ago
Updated over 2 years ago

grenaud/mappability_snpable

grenaud

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deML

Maximum likelihood demultiplexing

glactools

command-line tools for the management of genotype likelihoods and allele counts

leeHom

Bayesian reconstruction of ancient DNA fragments

gargammel

gargammel is an ancient DNA simulator

schmutzi

Maximum a posteriori estimate of contamination for ancient samples

vgan

Suite of tools for pangenomics built using vg

ROHan

Joint inference of heterozygosity rates and runs of homozygosity

freeIbis

An efficient basecaller for Illumina sequencers with calibrated quality scores

BCL2BAM2FASTQ

dice

Joint estimate of demography and contamination for nuclear ancient DNA

DNA2INT

quick benchmarking to check the best way to transform DNA letters to integers

aLib

insertsize

Simple C++ program built using samtools to get the insert size from BAM files

baselengthFilter

This program reads a BAM and produces another with a length filter applied on reads

VCFparser

C++ library for parsing VCF files

cinch

trieFinder

The trieFinder program is designed to rapidly map Digital Gene Expression (DGE) tags of various lengths to RefSeq, UniGene, and/or genomic sequences. It annotates the tags with information from the sequence files, providing output in a format that is amenable to both transcript quantification and the detection of novel transcripts.

SAFARI

Sensitive Alignments from a RYmer Index

libgab

A C++ class of useful little functions

bam2prof

the subprogram in schmutzi but rewritten using htslib

mitochondrialSimulator

A simple mitochondrial simulator