VSEARCH: a versatile open source tool for metagenomics
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Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, 25, 3389, 10.1093/nar/25.17.3389
Burge, 2013, Rfam 11.0: 10 years of RNA families, Nucleic Acids Research, 41, D226, 10.1093/nar/gks1005
Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nature Methods, 7, 335, 10.1038/nmeth.f.303
Cock, 2010, The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants, Nucleic Acids Research, 38, 1767, 10.1093/nar/gkp1137
DeSantis, 2006, Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB, Applied and Environmental Microbiology, 72, 5069, 10.1128/AEM.03006-05
Eastlake, 2001, US Secure Hash Algorithm 1 (SHA)
Edgar, 2010, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460, 10.1093/bioinformatics/btq461
Edgar, 2013, UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nature Methods, 10, 996, 10.1038/nmeth.2604
Edgar, 2015, Error filtering, pair assembly and error correction for next-generation sequencing reads, Bioinformatics, 31, 3476, 10.1093/bioinformatics/btv401
Edgar, 2011, UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, 27, 2194, 10.1093/bioinformatics/btr381
Fowler, 1991, Fowler / Noll / Vo (FNV) hash
Gailly, 2016, zlib: a massively spiffy yet delicately unobtrusive compression library
Gilbert, 2014, The Earth Microbiome project: successes and aspirations, BMC Biology, 12, 69, 10.1186/s12915-014-0069-1
Gusfield, 1993, Efficient methods for multiple sequence alignment with guaranteed error bounds, Bulletin of Mathematical Biology, 55, 141, 10.1007/BF02460299
He, 2015, Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity, Microbiome, 3, 10.1186/s40168-015-0081-x
Hirschberg, 1975, A linear space algorithm for computing maximal common subsequences, Communications of the ACM, 18, 341, 10.1145/360825.360861
Human Microbiome Project Consortium, 2012, Structure, function and diversity of the healthy human microbiome, Nature, 486, 207, 10.1038/nature11234
Karsenti, 2011, A holistic approach to marine eco-systems biology, PLoS Biology, 9, e1001177, 10.1371/journal.pbio.1001177
Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324
Logares, 2014, The patterning of rare and abundant community assemblages in coastal marine-planktonic microbial eukaryotes, Current Biology, 24, 813, 10.1016/j.cub.2014.02.050
MacCallum, 2009, ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads, Genome Biology, 10, R103, 10.1186/gb-2009-10-10-r103
Mahé, 2014, Swarm: robust and fast clustering method for amplicon-based studies, PeerJ, 2, e593, 10.7717/peerj.593
Masella, 2012, PANDAseq: paired-end assembler for illumina sequences, BMC Bioinformatics, 13, 31, 10.1186/1471-2105-13-31
Myers, 1988, Optimal alignments in linear space, Computer Applications in the Biosciences, 4, 11
Needleman, 1970, A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, 48, 443, 10.1016/0022-2836(70)90057-4
Nichols, 2016, Simera: Modelling the PCR Process to Simulate Realistic Chimera Formation, bioRxiv, 10.1101/072447
Quast, 2013, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Research, 41, D590, 10.1093/nar/gks1219
Rand, 1971, Objective criteria for the evaluation of clustering methods, Journal of the American Statistical Association, 66, 846, 10.2307/2284239
Rognes, 2011, Faster Smith-Waterman database searches by inter-sequence SIMD parallelisation, BMC Bioinformatics, 12, 221, 10.1186/1471-2105-12-221
Schirmer, 2015, Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform, Nucleic Acids Research, 43, e37, 10.1093/nar/gku1341
Schloss, 2016, Application of a database-independent approach to assess the quality of operational taxonomic unit picking methods, mSystems, 1, e00027, 10.1128/mSystems.00027-16
Schloss, 2009, Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities, Applied and Environmental Microbiology, 75, 7537, 10.1128/AEM.01541-09
Seward, 2016, bzip2 and libbzip2
Song, 2014, New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing, Briefings in Bioinformatics, 15, 343, 10.1093/bib/bbt067
Steffen, 2015, Sustainability. Planetary boundaries: guiding human development on a changing planet, Science, 347, 1259855, 10.1126/science.1259855
Westcott, 2015, De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units, PeerJ, 3, e1487, 10.7717/peerj.1487