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agouti

Annotated Genome Optimization Using Transcriptome Information

ancestry_hmm_pipeline

angsd

Program for analysing NGS data.

ascend

Method to estimate the age and intensity of recent bottlenecks/founder events, using genotype data and a recombination map.

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

dedup_merged_bams

Deduplicate alignments in BAMs merged from adjacent (possibly overlapping) regions. These duplicated alignments are generally artifacts of a scatter-gather process. (My first Rust project)

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

ega-download-client

A basic Python-based EGA download client

fastq_to_gvcf_nextflow

Nextflow pipeline for generating per-sample gVCFs from sequencing read FASTQs (initially implemented for human data following slight modifications of the GATK Best Practices)

finishingtool

finshingTool

gvcf_to_annotated_vcf_nextflow

Nextflow pipeline for generating multi-sample VQSR- and dbSNP-annotated VCFs from per-sample gVCFs generated by fastq_to_gvcf.nf. Also contains a pipeline for preparing dbSNP and archaic hominin VCFs for usage with hs37d5 modern human VCFs.

hapsnpeval

Simple evaluation of haplotypes reconstructed from simulated reads

hifiadapterfilt

Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).

humanpopgenscripts

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

jackalope

A swift, versatile phylogenomic and high-throughput sequencing simulator

low_depth_qc

Basic QC pipeline for low-depth Illumina data, mainly intended for human data and used for the PIBv1 dataset

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

msg

Multiplexed Shotgun Genotyping

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)

phase_final_vcf_nextflow

Phase multi-sample VCF using read-informed statistical phasing (i.e. WhatsHap for read-backed phasing, fed into SHAPEIT4 statistical phasing without reference panel) along with evaluation of phasing quality and error rates using trios.

pibv1_manuscript

Processing and analysis pipelines for the manuscript titled "Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania"

pseudoreferencepipeline

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

randomscripts

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

relate

Software for estimating genome-wide genealogies for thousands of samples

svmu

A pipeline to call structural variants from genome alignment

variantcallingsimulations

Variant Calling Simulation pipeline for diverged and polymorphic genomes