Scripts that contributed to the assembly and analysis of Urochloa decumbens

PhaseGrass, a reference-based phasing workflow generating chromosome-level haplotype-resolved diploid assembly for highly heterozygous genomes

A chromosome-level genome assembly of a avivorous bat (Nyctalus aviator)

A conda-forge distribution.

Lima - Demultiplex Barcoded PacBio Samples

Pipelines, code and ressources for creating a fully haplotype-resolved T2T assembly of the African catfish (Clarias gariepinus) combining PacBio HiFi, ONT long reads and Hi-C data.

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

An assembly pipeline that is designed to take raw input nanopore reads to assemblies ready for genome annotation

Apache Groovy: A powerful multi-faceted programming language for the JVM platform

📺 Discover the latest machine learning / AI courses on YouTube.

12 weeks, 26 lessons, 52 quizzes, classic Machine Learning for all

Scripts used for various genomic analyses, including assembly and annotation

convert various features into a GFF-like file for use in genome browsers

Protein hint generation pipeline for gene finding in eukaryotic genomes

A curated collection of Nextflow implementation patterns

Genome annotation with AUGUSTUS

Documentation of analyses and commands used as part of the PhD project investigating next generation diagnostics

Ultra-deep search for novel viruses

PASA software

This repo collects the list of learning online resources related to microbiome computational science and tools.

Pipelines used in my PhD/day-to-day

Workflow for read mapping and variant calling (GATK4) from Whole Genome Sequencing data of non-model species.

List of genome assembly tools

Machine Learning for Genomics Course.