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abrigahit

Snakefile for assembly of metagenomes with Megahit and resistome profiling with Abricate

amrplusplus_v2

MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-throughput sequencing data

anki-csv-importer

Import local or remote CSV files into Anki from the command line

atlas

ATLAS - Three commands to start analyzing your metagenome data

biochem-3bp3

Lectures and Lab Exercises for Biochem 3BP3 Practical Bioinformatics for the Genomics Era

bioinformatic-nextflow-pipelines

Collection of bioinformatic pipelines written in nextflow

bioinformatics_curriculum

Some ideas on things to learn to get started with bioinformatics

econ

ECON: Explicit Clothed humans Obtained from Normals

parse-atlas-gc

parse genecatalog from metagenome atlas

rgi

Snakefile to run Resistance Gene Identifier (RGI) on extracted SNPs from AMRPlusPlus v2.0.

shortbred_singularity_snakemake

Snakefile to run ShortBred using Singularity container

singularity_playground

This repo maintains the definition files used for building singularity images remotely. Each branch maintains a different environment.

snakefiles

workflows using snakemake

stag-mwc

StaG Metagenomic Workflow Collaboration

stag-sis

Singularity in Singularity container for StaG metagenomic workflow

termin-4-lakarprogrammet-ki

Ankidecks för Termin 4 Läkarprogrammet KI

termin-5-6-lakarprogrammet-ki

Ankidecks Termin 5 & 6 läkarprogrammet KI

termin-7-lakarprogrammet-ki

ublastx_stageone

This is the source code for multisamples ARGs profiling using SARG2.0 database