Sunday's Projects
3D de novo assembly (3D DNA) pipeline
A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curation issues.
to assess Metagenome assembly
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Conda recipes for the bioconda channel.
An algorithm for centromere assembly using long error-prone reads
deeplearning.ai , By Andrew Ng, All slide and notebook + code and some material.
The DevNet project on github stores the PacBio DevNet website.
Development version of Easyfig
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.
MGnify genome analysis pipeline
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
based on human gut microbial for machinelearning
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 analysis pipeline
Contains a fasta format database of a large variety of mobile genetic elements and an annotation file
Software for prediction of plasmid sequences in metagenomic assemblies
All Algorithms implemented in Python
Routines, Tools and Parsers
Fast and flexible genome assembly scaffolding
Tools (written in C using htslib) for manipulating next-generation sequencing data
Metagenomic pipeline and other general scripts used in the lab.
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Compute distance between sequences. 30+ algorithms, pure python implementation, common interface, optional external libs usage.