YourePrettyGood

RandomScripts

Collection of arbitrary (perhaps useful) programs and scripts, and occasional one-liners

PseudoreferencePipeline

Parallelized pipeline for alignment, variant calling, and generation of pseudoreference FASTAs from Illumina data (DNA- or RNAseq)

msg

Multiplexed Shotgun Genotyping

VariantCallingSimulations

Variant Calling Simulation pipeline for diverged and polymorphic genomes

AGOUTI

Annotated Genome Optimization Using Transcriptome Information

Ancestry_HMM_pipeline

angsd

Program for analysing NGS data.

DyakCladeGenomes

Scripts used for processing and analyses of PacBio genomes (and popgen samples mapped to these references) from the Drosophila yakuba clade (D. santomea, D. teissieri, and D. yakuba)

DyakInversions

Scripts used for analyses of inversions in Drosophila yakuba

HumanPopGenScripts

Scripts used for pre- and post-processing of various human population genomics analyses

blobtools

Application for the visualisation of draft genome assemblies and general QC

BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

CSVTranspose

Program to transpose large CSV files

ega-download-client

A basic Python-based EGA download client

finishingTool

finshingTool

HapSNPeval

Simple evaluation of haplotypes reconstructed from simulated reads

jackalope

A swift, versatile phylogenomic and high-throughput sequencing simulator

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

ncASE

Updated version of non-competitive Allele-Specific Expression method originally designed by Maria Gutin

ParsingPipeline

Illumina data parsing scripts (for use when i5 and/or i7 index reads are provided as separate synchronized FASTQs)

svmu

A pipeline to call structural variants from genome alignment