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agat

Another Gtf/Gff Analysis Toolkit

alppaca

A tooL for Prokaryotic Phylogeny And Clustering Analysis

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

book-compgenomr

broad-fungalgroup

Broad Fungal Genomics group scripts

c9-python-getting-started

Sample code for Channel 9 Python for Beginners course

calculate-haplotype-frequencies

This script calculates allelic and genotypic frequencies, as well as perform Fisher's Exact Test to compare representation of genotypes and alleles in different sample groups

clockwork

CRyPTIC data processing pipelines

compare_genomes

A comparative genomics workflow using Nextflow, conda, Julia and R

coverm

Read coverage calculator for metagenomics

diffcoexp

Differential coexpression analysis

eca-bioinf-handbook

Lecture notes/book in progress on computing for conservation genomics

ellipsis

Plasmid assembly, gene identification and annotation pipeline

emmtyper

emm Automatic Isolate Labeller

extract-haplotype-sequences

fastani

Fast Whole-Genome Similarity (ANI) Estimation

findfungi

A pipeline for the identification of fungi in public metagenomics datasets

freyja

Depth-weighted De-Mixing

hamronization

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

haplotypo

This is the Haplotypo repository

happy-git-with-r

Using Git and GitHub with R, Rstudio, and R Markdown

jekesa

Jekesa (Illuminate) is an automated bash pipeline for bacterial whole genome assembly and typing using Illumina paired-end sequencing data.

kingfisher-download

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

lncrna-analysis

mirna-analysis

Pipeline for miRNA profiling, including read mapping, multi-mapped read correction and read counting

mycosnp-nf

CDCgov/mycosnp-nf

nextflow_cheatsheet

Tips for Nextflow and cheatsheet for channel operation

ngi-rnaseq

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

pairwise_difference_count

Counts pairwise differences between sequences in DNA alignments