Beast code in Giters

jinhao94's starred repositories

DeepFRI

Deep functional residue identification

Language:PythonBSD-3-Clause289 10 42

PPanGGOLiN

Build a partitioned pangenome graph from microbial genomes

Language:PythonNOASSERTION232 13 129

sylph

ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.

Language:RustMIT130 3 14

referenceseeker

Rapid determination of appropriate reference genomes.

Language:PythonGPL-3.088 6 25

GenoVi

GenoVi, an automated customizable circular genome visualizer for bacteria and archaea

Language:PythonNOASSERTION76 4 20

bactmap

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Language:NextflowMIT50 136 25

panstripe

post processing of bacterial pangenome gene presence/absence matrices

Language:RGPL-2.048 2 15

mm2-fast

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Language:CNOASSERTION46 3 9

pantagruel

a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome

Language:PythonGPL-3.046 5 50

RabbitTClust

RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches

Language:C++NOASSERTION40 3 12

skDER

skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.

Language:PythonBSD-3-Clause37 1 5

MIDAS2

Metagenomic Intra-Species Diversity Analysis 2

Language:PythonMIT32 6 33

Codes and sample data supporting the Dutch Microbiome Project. The preprint is currently available at https://www.biorxiv.org/content/10.1101/2020.11.27.401125v1 and full data can be requested from EGA (https://ega-archive.org/studies/EGAS00001005027) and Lifelines biobank (https://www.lifelines.nl/researcher)

Language:HTML29 50

Maast

Microbial agile accurate SNP Typer

Language:PythonMIT29 2 27

COPD_multiomics

This repository contains computer codes for main analyses of the manuscript titled 'Multi-omic Landscape of Airway Microbe-Host Interaction in Chronic Obstructive Pulmonary Disease'.

Language:R27 10

fairy

alignment-free coverage calculation for metagenomic binning >100 times faster

Language:RustMIT25 2 2

ConQuR

Batch effects removal for microbiome data via conditional quantile regression

Language:RGPL-3.02500

partie

PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE allows automatic separation of the data.

Language:PerlMIT24 7 4

KEMET

KEGG Module Evaluation Tool

Language:PythonNOASSERTION24 3 15

Metagenome

Language:Python2300

score-assemblies

Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).

Language:PythonMIT23 3 10

SanntiS

SMBGC Annotation using Neural Networks Trained on Interpro Signatures

Language:PythonApache-2.01900

VFCs

Code for de novo discovery of viral families in virome data

Language:Perl13 1 3

Waters2mzML

Waters2mzML converts & subsequently annotates Waters .raw MSn data (both MSe & DDA) into functional .mzML files. Obtained .mzML files can be processed in MZmine 3. It would be interesting to see if it works for all Waters .raw data and other processing streamlines.

Language:PythonGPL-3.011 1 2

jinhao94