louiejtaylor

grabseqs

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

komplexity

A k-mer-based approach for masking low-complexity nucleotide sequences.

hisss

Snakemake workflow to download and/or align reads to targets and produce useful outputs.

pyviko

A web interface & Python tool to design knockouts in viruses with overlapping genes.

fang-tcga

Snakemake workflow to dump TCGA reads, map to target genomes, and summarize alignments

bioconda-recipes

Conda recipes for the bioconda channel.

cressdnaviricota_reps

find-prok-rbs

Looks for prokaryotic RBS upstream of ORFs given .gb files

github_tutorial

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

kz_conda

Conda recipe for komplexity (https://github.com/eclarke/komplexity/)

metagenomics-workshop

nanoflow

Bioinformatics pipeline for nanopore sequencing data

nanoflow.github.io

sbx_bahram2018

Sunbeam extension to reproduce key results from Bahram et al 2018 (PMID: 30069051)

sbx_dedup

Sunbeam extension

sbx_eggnog

sbx_kaiju

Kaiju metagenomics classifier for Sunbeam

sbx_kraken2

Sunbeam extension to run kraken2

sbx_kraken_uniq

sbx_lewis2015

Sunbeam extension to reproduce key results from Lewis et al 2015 (PMID: 26468751)

sbx_mccann2018

Sunbeam extension to reproduce key results from McCann et al 2018 (PMID: 29761040)

sbx_metaphlan

Sunbeam extension for running MetaPhlAn

sbx_minimap2

Sunbeam extension to run minimap2

sbx_report

Generates a final report, with figures, from a Sunbeam run

sbx_rgi

Sunbeam extension to run RGI (Resistance Gene Identifier)

sbx_select_coassembled_contigs

Sunbeam extension to select coassembled contigs with homology to a particular blast database

sbx_select_contigs

Selecting contigs after BLAST annotation

sunbeam

A robust, extensible metagenomics pipeline

sunbeam-labs.github.io

VODKA