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alignment-and-variant-calling-tutorial

basic walk-throughs for alignment and variant calling from NGS sequencing data

bioconda-recipes

Conda recipes for the bioconda channel.

bioinformaticsfromcoursera

brocc

Consensus taxonomy assignment for short reads (great for fungi)

cas13a_guide_design

cell-systems-2022

coresnps

cortex

reference free variant assembly

covid19-transcriptomics-pathogenesis-diagnostics-results

decontam

python3.5 version

decontam-1

dnabc

python3.5

dnabc-1

Identify DNA barcodes in high-throughput sequencing data files

dnabc_sunbeam

demultiplex Undetermined Fastq files, generate the data_fp folder for sunbeam. can be treated as the subworkflow of sunbeam.

dynamic_cdiff-bai-bsh

dynamic_ibd-abx

evd68

github_tutorial

A hands on forking, cloning, pulling, pushing, merging tutorial.

gro_bsh_bai

iggsearch

Metagenomic species profiling with enhanced coverage of the human gut microbiome

igram_strains

instrain

Bioinformatics program inStrain

mccortex

De novo genome assembly and multisample variant calling

midas-iggdb

An integrated pipeline for estimating strain-level genomic variation from metagenomic data, updated to cover 23,790 species from IGGdb.

midas2

Metagenomic Intra-Species Diversity Analysis 2

midas2-tutorial

midas2-wiki

Auxiliary repo for developing the MIDAS2 documentation

midas2_utils

Diagnostic and analysis scripts for MIDAS2

ml-pitfalls

Notebooks accompanying the paper "Navigating the pitfalls of applying machine learning in genomics"

mwas-project