Ayixon's repositories
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 "
abritAMR
A pipeline for running AMRfinderPlus and collating results into functional classes
Bactopia
A flexible pipeline for complete analysis of bacterial genomes
CASCABEL-16S
Automated pipeline for amplicon sequence analysis
chronumental
Estimating time trees from very large phylogenies
CRAQ-Assembly-Quality-
Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement
dadasnake-16S
Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
Fast-Fungal-Genome-Classifier
A tool for quickly and accurately classifying fungal genomes
genomescanner
Experimental tool to taxonomically classify microbial genomes in a few minutes
gggenomes
A grammar of graphics for comparative genomics
gNOMO2-multi-omics
gNOMO2 allows integrated multi-omics analyses of microbiomes
lotus2-16S
Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
LR-GapCloser
A gap-closing software tool that uses long reads to enhance genome assembly.
Mabs-AssemblerLR
Mabs, a genome assembly tool which optimizes parameters of Hifiasm and Flye
Mash-sketched-reference-databases
Mash-sketched reference databases are an up-to-date representation of several NCBI genomic, proteomic and metagenomic data, curated and formatted according to the sketching MinHash algorithm developed by Ondov et al. 2016. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x. Each dataset is in .msh format and mostly represents information from type material, in order to offer informative contexts with standard in nomenclature when possible.
MashMap
A fast approximate aligner for long DNA sequences
mcorr-recombination
Inferring bacterial recombination rates from large-scale sequencing datasets.
MuDoGeR
MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.
Natrix-16S
Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
Phylonium-Fast-Phylogenies-from-genomes
♥ Fast and Accurate Estimation of Evolutionary Distances
pimba-16S
PIMBA, a PIpeline for MetaBarcoding Analysis, which allows the use of customized databases, as well as other reference databases.
R-utils-and-Scripts
This repo includes various utilities and scripts to analyze microbial genomic data
ribbon_1.2
Ribbons extracts all copies of mRNA ribosomal 16s from bacteria or archaea genomes
rrap
Metagenomic Read Recruitment Pipeline
snaq-16s
Qiime2 snakemake pipeline
tourmaline-16S
Amplicon sequence processing workflow using QIIME 2 and Snakemake