Pinned Repositories
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
nglmr_SV
Snakemake pipeline for structural variant calling from Nanopore long reads using NGLMR for mapping and Sniffles for variant calling.
JamieCFreeman's Repositories
JamieCFreeman/nglmr_SV
Snakemake pipeline for structural variant calling from Nanopore long reads using NGLMR for mapping and Sniffles for variant calling.
JamieCFreeman/3prime-tag-seq
Snakemake pipeline for processing 3' tag RNA-seq data.
JamieCFreeman/adaptive_potential_sims
JamieCFreeman/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?
JamieCFreeman/AWD
JamieCFreeman/BioHPC_SNP_calling
From fastq to vcf, using Trimmomatic, bwa mem, and GATK tools.
JamieCFreeman/BSA
Scripts for bulked segregant analysis
JamieCFreeman/chtc_bwa_stampy
Testing w/ Jeremy's chtc implementation of the DGN style two-step mapping (bwa aln -> stampy)
JamieCFreeman/DGN_compatible
Pipeline to analyze DNA sequencing data with legacy compatibility for the Pool lab's Drosophila Genome Nexus data.
JamieCFreeman/dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
JamieCFreeman/dup_testing
JamieCFreeman/ena-fast-download
Download FASTQ files of reads from the European Nucleotide Archive (ENA)
JamieCFreeman/FAS1K_utils
Functions for handling the Pool labs .fas1k file format
JamieCFreeman/fly_kitchen_billing
Automate reading of Google sheet with fly kitchen orders to generate monthly user charges
JamieCFreeman/GAAS
Genome Assembly and Annotation Service code
JamieCFreeman/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.
JamieCFreeman/matt_mismatch
JamieCFreeman/nano-snakemake
A snakemake pipeline for SV analysis from nanopore genome sequencing
JamieCFreeman/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
JamieCFreeman/simulations_introgression_recombination
JamieCFreeman/snakemake_popoolation_BSA
JamieCFreeman/snakemake_SRA_metadata_fetch
JamieCFreeman/utils
A collection of scripts that I use often for working with omics type analyses.