The Conventional Commits toolbox

whofluIRMA - influenza assembly pipeline

Miscellaneous data manipulation tools

📚 Parameterize, execute, and analyze notebooks

Examples that illustrate how nbconvert can be used

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Step by step tutorial using chewBBACA with all necessary files and results

LAMBDA – the Local Aligner for Massive Biological DatA

Order and orientation of complete bacterial genomes

Quality control for MinION sequencing data

catalog for long-read sequencing tools

BSR-Based Allele Calling Algorithm

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/Gra…

Generate Google Slides from markdown

🍊 🕸 Network analysis add-on for Orange data mining suite.

Graphical Fragment Assembly (GFA) Format Specification

A tool to easily create informative genomic feature plots

RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.

Chromosome-level scaffolding using multiple references

hybrid assembly pipeline for bacterial genomes

De novo assembler for single molecule sequencing reads using repeat graphs

MITObim - mitochondrial baiting and iterative mapping

Pan-genome inference and genotyping with long noisy or short accurate reads

Quick and dirty scripts used in my bioinformatics adventures

Filtering and trimming of long read sequencing data