ntjoin

🔗Genome assembly scaffolder using minimizer graphs

orthofisher

a broadly applicable tool for automated gene identification and retrieval

parallel-meta

A High Performance Microbiome Analysis Toolkit.

perl-for-reysenbach-lab

These are perl scripts I developed over many years as a Bioinformaticist for the Reysenbach Lab at PSU. The Reysenbach Lab studies microbial diversity in extreme environments. Lotta fasta utilities here if you are into that sort of thing.

phylonium-fast-phylogenies-from-genomes

♥ Fast and Accurate Estimation of Evolutionary Distances

pilon

Pilon is an automated genome assembly improvement and variant detection tool

pimba-16s

PIMBA, a PIpeline for MetaBarcoding Analysis, which allows the use of customized databases, as well as other reference databases.

pocp

Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014

proovframe

frame-shift correction for long-read (meta)genomics

pseudofinder

Detection of pseudogene candidates in bacterial and archaeal genomes.

ptp

PTP model for species delimitation

quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

r-utils-and-scripts

This repo includes various utilities and scripts to analyze microbial genomic data

rapdtool

Rapid Profiling and Deconvolution Tool for Metagenomes

redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

ribbon_1.2

Ribbons extracts all copies of mRNA ribosomal 16s from bacteria or archaea genomes

rrap

Metagenomic Read Recruitment Pipeline

semibin

seq-scripts

scripts for sequence and feature conversion, annotation, analysis ...

sequel-assembly-correcting-tool

SEQuel is a tool for correcting errors (i.e., insertions, deletions, and substitutions) in contigs output from assembly. All credits to: Roy Ronen, Christina Boucher, Hamidreza Chitsaz, Pavel Pevzner, SEQuel: improving the accuracy of genome assemblies, Bioinformatics, Volume 28, Issue 12, 15 June 2012, Pages i188–i196, https://doi.org/10.1093/bioinformatics/bts219

snaq-16s

Qiime2 snakemake pipeline

tapestry

Validate and edit small eukaryotic genome assemblies

tourmaline-16s

Amplicon sequence processing workflow using QIIME 2 and Snakemake

treegwas

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes

trycycler

A tool for generating consensus long-read assemblies for bacterial genomes

useful_scripts

whokaryote

Classify metagenomic contigs as eukaryotic or prokaryotic

workflow-to-reproduce-bp6-2022-paper

Methods and scripts to reproduce: "Biodegradation of a polyether-polyurethane-acrylic copolymer by a landfill microbial community. Genetic basis inferred from metagenomic deconvolution analysis "