metagenomes 开源项目推荐（41 个）

jtamames /SqueezeMeta

A complete pipeline for metagenomic analysis

nf-core /mag

Assembly and binning of metagenomes

althonos /pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

smaegol /PlasFlow

Software for prediction of plasmid sequences in metagenomic assemblies

GenomicsStandardsConsortium /mixs

Minimum Information about any (X) Sequence” (MIxS) specification

muellan /metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Shamir-Lab /Recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir

mtisza1 /Cenote-Taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)

cafferychen777 /MicrobiomeStat

追踪、分析、可视化：用MicrobiomeStat揭开你的微生物组的时间模式

SamStudio8 /gretel

An algorithm for recovering haplotypes from metagenomes

althonos /pyskani

PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.

linsalrob /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.

althonos /pyfastani

Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

Shamir-Lab /Faucet

This is the codebase for Faucet, described in our manuscript: https://academic.oup.com/bioinformatics/article/34/1/147/4004871, by Roye Rozov, Gil Goldshlager, Eran Halperin, and Ron Shamir

SegataLab /preprocessing

Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination

marbl /MetaCarvel

MetaCarvel: A scaffolder for metagenomes

Chartiza /Microbiome

scripts for microbiome analysis

metageni /FOCUS

FOCUS: An Agile Profiler for Metagenomic Data

daasabogalro /PopMAG

Population genomics analyses from metagenome-assembled genomes

cafferychen777 /MicrobiomeStat-Turtorial-Professional-Version

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.