Pinned Repositories
bioconda-recipes
Conda recipes for the bioconda channel.
cressdnaviricota_reps
fang-tcga
Snakemake workflow to dump TCGA reads, map to target genomes, and summarize alignments
find-prok-rbs
Looks for prokaryotic RBS upstream of ORFs given .gb files
github_tutorial
A hands on forking, cloning, pulling, pushing, merging tutorial.
grabseqs
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
hisss
Snakemake workflow to download and/or align reads to targets and produce useful outputs.
komplexity
A k-mer-based approach for masking low-complexity nucleotide sequences.
pyviko
A web interface & Python tool to design knockouts in viruses with overlapping genes.
sunbeam
A robust, extensible metagenomics pipeline
louiejtaylor's Repositories
louiejtaylor/grabseqs
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
louiejtaylor/komplexity
A k-mer-based approach for masking low-complexity nucleotide sequences.
louiejtaylor/hisss
Snakemake workflow to download and/or align reads to targets and produce useful outputs.
louiejtaylor/pyviko
A web interface & Python tool to design knockouts in viruses with overlapping genes.
louiejtaylor/fang-tcga
Snakemake workflow to dump TCGA reads, map to target genomes, and summarize alignments
louiejtaylor/bioconda-recipes
Conda recipes for the bioconda channel.
louiejtaylor/cressdnaviricota_reps
louiejtaylor/find-prok-rbs
Looks for prokaryotic RBS upstream of ORFs given .gb files
louiejtaylor/github_tutorial
A hands on forking, cloning, pulling, pushing, merging tutorial.
louiejtaylor/kz_conda
Conda recipe for komplexity (https://github.com/eclarke/komplexity/)
louiejtaylor/metagenomics-workshop
louiejtaylor/nanoflow
Bioinformatics pipeline for nanopore sequencing data
louiejtaylor/nanoflow.github.io
louiejtaylor/sbx_bahram2018
Sunbeam extension to reproduce key results from Bahram et al 2018 (PMID: 30069051)
louiejtaylor/sbx_dedup
Sunbeam extension
louiejtaylor/sbx_eggnog
louiejtaylor/sbx_kaiju
Kaiju metagenomics classifier for Sunbeam
louiejtaylor/sbx_kraken2
Sunbeam extension to run kraken2
louiejtaylor/sbx_kraken_uniq
louiejtaylor/sbx_lewis2015
Sunbeam extension to reproduce key results from Lewis et al 2015 (PMID: 26468751)
louiejtaylor/sbx_mccann2018
Sunbeam extension to reproduce key results from McCann et al 2018 (PMID: 29761040)
louiejtaylor/sbx_metaphlan
Sunbeam extension for running MetaPhlAn
louiejtaylor/sbx_minimap2
Sunbeam extension to run minimap2
louiejtaylor/sbx_report
Generates a final report, with figures, from a Sunbeam run
louiejtaylor/sbx_rgi
Sunbeam extension to run RGI (Resistance Gene Identifier)
louiejtaylor/sbx_select_coassembled_contigs
Sunbeam extension to select coassembled contigs with homology to a particular blast database
louiejtaylor/sbx_select_contigs
Selecting contigs after BLAST annotation
louiejtaylor/sunbeam
A robust, extensible metagenomics pipeline
louiejtaylor/sunbeam-labs.github.io
louiejtaylor/VODKA