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16s_emu_pipeline

acanthophis

A comprehensive, opinionated plant variant calling pipeline in Snakemake

bioconda-recipes

Conda recipes for the bioconda channel.

coatofarms

ONT Long-read 16S Snakemake pipeline using Emu

crs_saureus_evolutionary_landscape

Repository to Hold Code base for 'The Intra-Host Evolutionary Landscape And Pathoadaptation Of Persistent Staphylococcus aureus In Chronic Rhinosinusitis' Paper

depth_vs_polishing_analysis

Repository to hold code and data for the How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies manuscript

dnaapler

Reorients assembled microbial sequences

general_rna_seq_pipeline

Pipeline to Generate TPM Counts using RNA Seq data using STAR, Salmon and Kallisto

giantpandrna

ONT Long-read cDNA quanitification pipeline using Bambu

hafez

A tool for identifying active prophage elements through read mapping

hlbroken

Identification and Extraction of s aureus hlb gene disruptions

hybracter

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

hybracter_benchmarking

Benchmarking Pipeline for Hybracter

koverage

Quickly get coverage statistics given reads and an assembly

megapharokka

A fork of Pharokka to handle enVhogs

nanopore_bacterial_assembly_pipeline

Pipeline to assemble many bacterial assemblies from Nanopore data

nanopore_rna_seq_cdna_pipeline

nanoreceptor

Program to infer IG and TRA quantities from Long Read RNA-Seq Data

pharokka

fast phage annotation program

phicore

work in progress. but got to do with phage genomes because they are awesome!

phold

Phage Annotation using Protein Structures

phynteny

Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny

plassembler

Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates

plassembler_simulation_benchmarking

Benchmarking and Simulation Scripts for Plassembler

prostt5

Bilingual Language Model for Protein Sequence and Structure

pypolca

Standalone Python re-implementation of the POLCA polisher from MaSuRCA

rna_seq_deconv_pipeline

s_aureus_analysis_pipeline

Analysis of S Aureus WGS Isolates

single_marker_gene_microbiome_analysis

Repository to hold analysis for single marker genes in HNSC Microbiome

spae

NEW!!! Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!