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...in metagenomics classification. KrakenUniq (formerly KrakenHLL) is a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with ...tral.com/articles/10.1186/s13059-018-1568-0 KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Breitwieser FP, Baker DN, Salzber

[[Category:Software]][[Category:Biology]][[Category:Metagenomics]] ...se and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. CoverM calculates coverage of genomes/MAGs or individual cont

The goal of many metagenomics studies is to characterize the content and relative abundance of sequences Often, metagenomics is performed when the answer to these questions must be obtained for a larg

...ple. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to ..., (2015) MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, doi: 10.1093/bioinfo

Reference-free Binning of Metagenomics Long Reads using Coverage and Composition title = "{MetaBCC-LR: metagenomics binning by coverage and composition for long reads}",

Taxonomic classification for metagenomics with deep learning.

title = {{LRBinner: Binning Long Reads in Metagenomics Datasets}}, annote = {Keywords: Metagenomics binning, long reads, machine learning, clustering}

BMTagger aka Best Match Tagger is for removing human reads from metagenomics datasets

SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins

Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several

...thod for determining replication rates for bacteria from single time point metagenomics sequencing and draft-quality genomes.

...el Microbial Detection and Quantification with Applications to Single Cell Metagenomics. Kaiyuan Zhu, Welles Robinson, Alejandro A. Schäffer, Junyan Xu, Eytan Rup

S Nayfach, B Rodriguez-Mueller, N Garud, and KS Pollard. "An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and gl

...lassification tool for short-read data designed to deal with large DNA/RNA metagenomics samples. Its performance and comprehensiveness makes it highly suitable for

...q (mainly for host-pathogen, symbiont and cohabitant interaction studies), metagenomics studies, sequencing and analysis of hybrid species, allele-specific express

...utes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers

...Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in

Metagenomics can provide important insight into microbial communities. However, assembli

Recent metagenomics studies of environmental samples suggest that microbial