Ayixon's Projects
A pipeline for running AMRfinderPlus and collating results into functional classes
AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
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
Amplicon sequencing of marker genes such as 16S rDNA
Improve the quality of a denovo assembly by scaffolding and gap filling
A list of interesting genome browser or genome-browser-like implementations
A flexible pipeline for complete analysis of bacterial genomes
BiGMeC - Biosynthetic Gene cluster Metabolic pathway Constructor
My bioinfo toolbox
Some useful python scripts for biologists
Conda recipes for the bioconda channel.
Bioinformatics Tools
CAMITAX: Taxon labels for microbial genomes
Automated pipeline for amplicon sequence analysis
Estimating time trees from very large phylogenies
A tool to circularize genome assemblies
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
Taxonomic classification of metagenomic contigs
Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement
Super-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references
A Java-based statistical framework for integration of shotgun metagenomics with other omics technologies
Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
A tool for quickly and accurately classifying fungal genomes
URMAP ultra-fast read mapper
finshingTool
Gapless provides combined scaffolding, gap-closing and assembly correction with long reads