A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.

A template for science projects. 🧑‍🔬📊

A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs

A tool for generating consensus long-read assemblies for bacterial genomes

Close assembly gaps using long-reads at high accuracy.

BAM Statistics, Feature Counting and Annotation

Metalign: efficient alignment-based metagenomic profiling via containment min hash

De novo long read scrubbing with Minimap and Convolutional Neural Networks

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

VICE jupyter lab with snakemake-minimal

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Data and analysis for NA12878 genome on nanopore

Fast genome analysis from unassembled short reads

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

A fast whole-genome aligner based on de Bruijn graphs

Graph based multi genome aligner

A versatile aligning pipeline for bisulfite sequencing data

NCBI Prokaryotic Genome Annotation Pipeline

Clustering cONtigs with COverage and ComposiTion

Taxon-aware analysis of clustered protein sequences

Workflows I find helpful for fungal genome annotation

ONT assembly and Illumina polishing pipeline

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

The Moby Project - a collaborative project for the container ecosystem to assemble container-based systems

Turn repositories into Jupyter-enabled Docker images

Ready-to-run Docker images containing Jupyter applications

sequence element (kmer) enrichment analysis

Beyond the consensus NGS tools

basic walk-throughs for alignment and variant calling from NGS sequencing data

Very very long reads, indeed