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MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets.

Reddy RM, Mohammed MH, Mande SS. Reddy RM, et al. Genomics. 2014 Feb-Mar;103(2-3):161-8. doi: 10.1016/j.ygeno.2014.02.007. Epub 2014 Mar 5. Genomics. 2014. PMID: 24607570 Free article.

COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets.

Bose T, Haque MM, Reddy C, Mande SS. Bose T, et al. PLoS One. 2015 Nov 11;10(11):e0142102. doi: 10.1371/journal.pone.0142102. eCollection 2015. PLoS One. 2015. PMID: 26561344 Free PMC article.

Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly.

Ghosh TS, Mehra V, Mande SS. Ghosh TS, et al. J Bioinform Comput Biol. 2015 Jun;13(3):1541004. doi: 10.1142/S0219720015410048. Epub 2015 Feb 8. J Bioinform Comput Biol. 2015. PMID: 25790784

A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes.

Gkanogiannis A, Gazut S, Salanoubat M, Kanj S, Brüls T. Gkanogiannis A, et al. BMC Bioinformatics. 2016 Aug 19;17(1):311. doi: 10.1186/s12859-016-1186-3. BMC Bioinformatics. 2016. PMID: 27542753 Free PMC article.

DIME: a novel framework for de novo metagenomic sequence assembly.

Guo X, Yu N, Ding X, Wang J, Pan Y. Guo X, et al. J Comput Biol. 2015 Feb;22(2):159-77. doi: 10.1089/cmb.2014.0251. J Comput Biol. 2015. PMID: 25684202 Free PMC article.

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices.

Li D, Luo R, Liu CM, Leung CM, Ting HF, Sadakane K, Yamashita H, Lam TW. Li D, et al. Methods. 2016 Jun 1;102:3-11. doi: 10.1016/j.ymeth.2016.02.020. Epub 2016 Mar 21. Methods. 2016. PMID: 27012178 Review.

Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

Huson DH, Tappu R, Bazinet AL, Xie C, Cummings MP, Nieselt K, Williams R. Huson DH, et al. Microbiome. 2017 Jan 25;5(1):11. doi: 10.1186/s40168-017-0233-2. Microbiome. 2017. PMID: 28122610 Free PMC article.

Recovering complete and draft population genomes from metagenome datasets.

Sangwan N, Xia F, Gilbert JA. Sangwan N, et al. Microbiome. 2016 Mar 8;4:8. doi: 10.1186/s40168-016-0154-5. Microbiome. 2016. PMID: 26951112 Free PMC article. Review.

OGRE: Overlap Graph-based metagenomic Read clustEring.

Balvert M, Luo X, Hauptfeld E, Schönhuth A, Dutilh BE. Balvert M, et al. Bioinformatics. 2021 May 17;37(7):905-912. doi: 10.1093/bioinformatics/btaa760. Bioinformatics. 2021. PMID: 32871010 Free PMC article.

Estimating the composition of species in metagenomes by clustering of next-generation read sequences.

Seok HS, Hong W, Kim J. Seok HS, et al. Methods. 2014 Oct 1;69(3):213-9. doi: 10.1016/j.ymeth.2014.07.009. Epub 2014 Jul 27. Methods. 2014. PMID: 25072168

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