Pinned Repositories
-Perfect--bacterial-genome-tutorial
abritAMR
A pipeline for running AMRfinderPlus and collating results into functional classes
amptk
AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
Apollo
Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described in the Bioinformatics journal paper (2020) by Firtina et al. at https://people.inf.ethz.ch/omutlu/pub/apollo-technology-independent-genome-assembly-polishing_bioinformatics20.pdf
asap2_16-S
Amplicon sequencing of marker genes such as 16S rDNA
ayixon
bit
Bioinformatics Tools
LongStitch
Correct and scaffold assemblies using long reads
RaPDTool
Rapid Profiling and Deconvolution Tool for Metagenomes
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 "
ayixon's Repositories
ayixon/RaPDTool
Rapid Profiling and Deconvolution Tool for Metagenomes
ayixon/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 "
ayixon/-Perfect--bacterial-genome-tutorial
ayixon/Asteroid-Tree
ayixon/Bactopia
A flexible pipeline for complete analysis of bacterial genomes
ayixon/CASCABEL-16S
Automated pipeline for amplicon sequence analysis
ayixon/chronumental
Estimating time trees from very large phylogenies
ayixon/CRAQ-Assembly-Quality-
Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement
ayixon/cviewerAllgenomicMeta
A Java-based statistical framework for integration of shotgun metagenomics with other omics technologies
ayixon/dadasnake-16S
Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
ayixon/Fast-Fungal-Genome-Classifier
A tool for quickly and accurately classifying fungal genomes
ayixon/genomescanner
Experimental tool to taxonomically classify microbial genomes in a few minutes
ayixon/gggenomes
A grammar of graphics for comparative genomics
ayixon/gNOMO2-multi-omics
gNOMO2 allows integrated multi-omics analyses of microbiomes
ayixon/lotus2-16S
Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
ayixon/LR-GapCloser
A gap-closing software tool that uses long reads to enhance genome assembly.
ayixon/Mabs-AssemblerLR
Mabs, a genome assembly tool which optimizes parameters of Hifiasm and Flye
ayixon/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.
ayixon/MashMap
A fast approximate aligner for long DNA sequences
ayixon/Masurca
ayixon/mcorr-recombination
Inferring bacterial recombination rates from large-scale sequencing datasets.
ayixon/MetaTranscriptomePipe
ayixon/MICROPHERRET
MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using machine lEarning Techniques
ayixon/MuDoGeR
MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.
ayixon/Natrix-16S
Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
ayixon/Phylonium-Fast-Phylogenies-from-genomes
♥ Fast and Accurate Estimation of Evolutionary Distances
ayixon/pimba-16S
PIMBA, a PIpeline for MetaBarcoding Analysis, which allows the use of customized databases, as well as other reference databases.
ayixon/R-utils-and-Scripts
This repo includes various utilities and scripts to analyze microbial genomic data
ayixon/snaq-16s
Qiime2 snakemake pipeline
ayixon/tourmaline-16S
Amplicon sequence processing workflow using QIIME 2 and Snakemake