JamieCFreeman

nglmr_SV

Snakemake pipeline for structural variant calling from Nanopore long reads using NGLMR for mapping and Sniffles for variant calling.

3prime-tag-seq

Snakemake pipeline for processing 3' tag RNA-seq data.

adaptive_potential_sims

Allele_competition_genetic_drift_sims

Can we distinguish selection from genetic drift? Looking at changing allele frequencies over time at a single locus, can the magnitude of change be explained by fluctuations due to random sampling?

AWD

BioHPC_SNP_calling

From fastq to vcf, using Trimmomatic, bwa mem, and GATK tools.

BSA

Scripts for bulked segregant analysis

chtc_bwa_stampy

Testing w/ Jeremy's chtc implementation of the DGN style two-step mapping (bwa aln -> stampy)

DGN_compatible

Pipeline to analyze DNA sequencing data with legacy compatibility for the Pool lab's Drosophila Genome Nexus data.

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

dup_testing

ena-fast-download

Download FASTQ files of reads from the European Nucleotide Archive (ENA)

FAS1K_utils

Functions for handling the Pool labs .fas1k file format

GAAS

Genome Assembly and Annotation Service code

inv_gt_PCA

Snakemake pipeline to generate a genotype matrix for the breakpoint regions around inversions from a panel of .fas1k files, run smartpca, and call inversion status of unknown samples.

matt_mismatch

nano-snakemake

A snakemake pipeline for SV analysis from nanopore genome sequencing

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

simulations_introgression_recombination

snakemake_popoolation_BSA

snakemake_SRA_metadata_fetch

utils

A collection of scripts that I use often for working with omics type analyses.