YourePrettyGood

AGOUTI

Annotated Genome Optimization Using Transcriptome Information

Ancestry_HMM_pipeline

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

msg

Multiplexed Shotgun Genotyping

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.

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

VariantCallingSimulations

Variant Calling Simulation pipeline for diverged and polymorphic genomes

YourePrettyGood/RandomScripts

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

YourePrettyGood/HumanPopGenScripts

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

YourePrettyGood/PseudoreferencePipeline

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

YourePrettyGood/msg

Multiplexed Shotgun Genotyping

YourePrettyGood/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.

YourePrettyGood/VariantCallingSimulations

Variant Calling Simulation pipeline for diverged and polymorphic genomes

YourePrettyGood/AGOUTI

Annotated Genome Optimization Using Transcriptome Information

YourePrettyGood/Ancestry_HMM_pipeline

YourePrettyGood/angsd

Program for analysing NGS data.

YourePrettyGood/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)

YourePrettyGood/DyakInversions

Scripts used for analyses of inversions in Drosophila yakuba

YourePrettyGood/ASCEND

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

YourePrettyGood/blobtools

Application for the visualisation of draft genome assemblies and general QC

YourePrettyGood/BRAKER

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

YourePrettyGood/CSVTranspose

Program to transpose large CSV files

YourePrettyGood/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)

YourePrettyGood/ega-download-client

A basic Python-based EGA download client

YourePrettyGood/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)

YourePrettyGood/finishingTool

finshingTool

YourePrettyGood/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.

YourePrettyGood/HapSNPeval

Simple evaluation of haplotypes reconstructed from simulated reads

YourePrettyGood/HiFiAdapterFilt

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

YourePrettyGood/jackalope

A swift, versatile phylogenomic and high-throughput sequencing simulator

YourePrettyGood/low_depth_QC

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

YourePrettyGood/lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

YourePrettyGood/ncASE

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

YourePrettyGood/ParsingPipeline

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

YourePrettyGood/PIBv1_manuscript

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

YourePrettyGood/relate

Software for estimating genome-wide genealogies for thousands of samples

YourePrettyGood/svmu

A pipeline to call structural variants from genome alignment