malonge

RagTag

Tools for fast and flexible genome assembly scaffolding and improvement

RaGOO

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

CallSV

A long-read SV calling pipeline

AlignmentConverters

Convert between common sequence alignment formats

PatchPolish

ChromMatch

Assign chromosome names to a genome assembly

DupCheck

Genotype putative DUPs by querying short read coverage

old_malonge.github.io

seqtk

Toolkit for processing sequences in FASTA/Q formats

T2T-Polish

Repository for the T2T CHM13 team-polishing group

Assemblytics_web

Full web application code for Assemblytics

bioconda-recipes

Conda recipes for the bioconda channel.

CallIntrogressions

CAMSA

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

FALCON

FALCON: experimental PacBio diploid assembler

hmmlearn

Hidden Markov Models in Python, with scikit-learn like API

malonge.github.io

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

Minipolish

A tool for Racon polishing of miniasm assemblies

NanoGrid

Nanopolish wrapper for SGE

SALSA

SALSA: A tool to scaffold long read assemblies with Hi-C data