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3d-dna

3D de novo assembly (3D DNA) pipeline

amr_curation

A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curation issues.

asmetagenome-assesment

to assess Metagenome assembly

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

bioconda-recipes

Conda recipes for the bioconda channel.

bioinformatics

centroflye

An algorithm for centromere assembly using long error-prone reads

deeplearning.ai

deeplearning.ai , By Andrew Ng, All slide and notebook + code and some material.

devnet

The DevNet project on github stores the PacBio DevNet website.

easyfig

Development version of Easyfig

ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

genomes-pipeline

MGnify genome analysis pipeline

harvest-tools

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

machelearing

based on human gut microbial for machinelearning

metagem

A Snakemake pipeline for the generation of MAGs, reconstruction of GEMs, and simulation of cross-feeding interactions within microbial communities from lab cultures, human gut, ocean, plant-associated, and bulk soil microbiomes

metagenome

Metagenome analysis pipeline

mobilegeneticelementdatabase

Contains a fasta format database of a large variety of mobile genetic elements and an annotation file

plasflow

Software for prediction of plasmid sequences in metagenomic assemblies

python

All Algorithms implemented in Python

pytools_bio

Routines, Tools and Parsers

ragtag

Fast and flexible genome assembly scaffolding

reporterscore_metagenomics

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

scripts

Metagenomic pipeline and other general scripts used in the lab.

staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

textdistance

Compute distance between sequences. 30+ algorithms, pure python implementation, common interface, optional external libs usage.

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