YourePrettyGood
Postdoc working in human evolutionary genomics, used to work in population genomics of Drosophila and Lepidoptera, unreasonably fond of awk
Pinned Repositories
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
msg
Multiplexed Shotgun Genotyping
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's Repositories
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/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/finishingTool
finshingTool
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/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/relate
Software for estimating genome-wide genealogies for thousands of samples
YourePrettyGood/svmu
A pipeline to call structural variants from genome alignment