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Brief Bio

Microbiologist apprentice. Farmer by birth. I have seen the leaf and the stem of the cane, the coffee bean, since it is a white and aromatic flower bud. In biology, the Darwin of Shrewsbury and Cavalier-Smith. The mystery of the species in prokaryotes, its concepts and demarcations would make any biologist happy or miserable.

The best story: "The immortal" (by Borges ...). The best novel: "100 years of solitude" (García Márquez)

The best poem: ... I'm not so crazy to risk that answer; but once I told myself that Whitman in the North and Vallejo in the South. In the movies: Clint Eastwood. In music: EL SON ... the one that comes from Nené Manfugás.

And of course, microbial taxonomy and metabolism of xenobiotics

Ayixon's Projects

abritamr icon abritamr

A pipeline for running AMRfinderPlus and collating results into functional classes

amptk icon amptk

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

apollo icon 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 icon asap2_16-s

Amplicon sequencing of marker genes such as 16S rDNA

bactopia icon bactopia

A flexible pipeline for complete analysis of bacterial genomes

bigmec icon bigmec

BiGMeC - Biosynthetic Gene cluster Metabolic pathway Constructor

bio-py icon bio-py

Some useful python scripts for biologists

bit icon bit

Bioinformatics Tools

camitax icon camitax

CAMITAX: Taxon labels for microbial genomes

clonalframeml icon clonalframeml

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

contigtax icon contigtax

Taxonomic classification of metagenomic contigs

craq-assembly-quality- icon craq-assembly-quality-

Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement

cross-species-scaffolding icon cross-species-scaffolding

Super-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references

dadasnake-16s icon dadasnake-16s

Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake

dram icon dram

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

gapless icon gapless

Gapless provides combined scaffolding, gap-closing and assembly correction with long reads

gappadder icon gappadder

GAPPadder is tool for closing gaps on draft genomes with short sequencing data

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