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16s-rdna-dada2-pipeline

**DEFUNCT** dada2-based Nextflow pipeline for multiple amplicon data. See website for up-to-date version

allan-fluidigm-pipeline

allele_frequency

Allele frequency of codons in specific targeted regions of the mouse genome

bacterial_variant_calling

A pipeline for variant calling on bacterial genomes created with Nextflow and singularity / docker

bamreadcountr

wrapper and parser for bam readcount

bashwes_varcall_bw

Bash-glued variant calling workflow optimized for WES on Blue Waters

bio-lowlevel-samtools

Low-level (XS) bindings to Samtools

bioperl-pipeline

Analysis pipelines from wrappers

bw_variantcalling

A flexible workflow to run variant calling at the scale of hundreds of genomes

caceres-16s-mosquito-2022sept

chipseq

Chromatin immunoprecipitation (ChIP-seq) analysis using BWA and MACS2 with QC steps.

coi_ncbi_2018

This repository contains the scripts used to retrieve and analyze the data reported in Porter & Hajibabaei 2018 bioRxiv doi: https://doi.org/10.1101/353904

configs

Config files used to define parameters specific to compute environments at different Institutions

cpg

Building a Chinese pan-genome of 486 individuals

cut-and-run

cutandrun

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

data-management

Data Carpentry data management course, combining CSE and HPCBio materials

datamgmt

Workshop covering principles of data management. Gaps in the Git material are intended to be filled with Software Carpentry's git-novice lesson.

detect-seq

An unbiased method for genome-wide CBE off-targets assessment

diffreps

Differential analysis for ChIP-seq with biological replicates

eib-marker-design

Workflow for designing KASP markers from resequencing data

em-seq

Tools and Data related to Enzymatic Methylation Sequencing

emirge

EMIRGE reconstructs full length ribosomal genes from short read sequencing data.

figaro

An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters

gff3toolkit

Python programs for processing GFF3 files

h3abionet16s

H3ABioNet 16S package

haplomerger2

Haplomerger2 (v20180603)

haplomerger2-dev

Hacked version of HaploMerger using .2bit databases

hclust2

Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication.

hergenrother-16s-mouse-2022sept

Code for the Hergenrother 2022 mouse antimicrobiall study