JamieCFreeman's repositories
3prime-tag-seq
Snakemake pipeline for processing 3' tag RNA-seq data.
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?
BioHPC_SNP_calling
From fastq to vcf, using Trimmomatic, bwa mem, and GATK tools.
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
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.
nano-snakemake
A snakemake pipeline for SV analysis from nanopore genome sequencing
rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2