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

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

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

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 phasin…

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 VC…

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

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)

Scripts used for analyses of inversions in Drosophila yakuba

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)

Variant Calling Simulation pipeline for diverged and polymorphic genomes

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

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

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

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

Simple evaluation of haplotypes reconstructed from simulated reads

Program to transpose large CSV files