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
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Updated
May 21, 2017 - C++
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
CWL implementation for DEMIC
To reproduce some results from "CAMISIM: simulating metagenomes and microbial communities". Authors: Simon Konnov, Ciara Makievskaya, Ruslan Gumerov
A few scripts to help with the installation of MetaErg, the contig/bin annotation pipeline
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes
Code associated with the Ley Lab animal gut metagenome assembly project
Application of Recurrent Neural Network to Metagenomic
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
Software for prediction of plasmid sequences in metagenomic assemblies
An algorithm for recovering haplotypes from metagenomes
MetaCarvel: A scaffolder for metagenomes
FOCUS: An Agile Profiler for Metagenomic Data
This project aims do describe and explore the metagenomes of fern species of the genus Azolla.
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.
XGBoost implementation for bacteria family identification
Arche: a functional-optimized annotator for microbial meta(genomes)
Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
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