VSEARCH: a versatile open source tool for metagenomics
Citations
2,791 citations
2,475 citations
Cites background or methods from "VSEARCH: a versatile open source to..."
...Naive Bayes (0.022984 s/ sequence), BLAST+ (0.026222 s/sequence), and VSEARCH (0.030190 s/sequence) exhibit greater slopes....
[...]
...The naive Bayes, VSEARCH, and BLAST+ consensus classifiers described here are released for the first time in QIIME 2, with optimized “balanced” configurations (Table 2) set as defaults....
[...]
...The methods classify_consensus_vsearch and classify_consensus_blast use the global aligner VSEARCH [10] or the local aligner BLAST+ [9], respectively, to return up to maxaccepts reference sequences that align to the query with at least perc_identity similarity....
[...]
...The q2feature-classifier plugin supports use of any of the numerous machine-learning classifiers available in scikitlearn [7, 8] for marker gene taxonomy classification, and currently provides two alignment-based taxonomy consensus classifiers based on BLAST+ [9] and VSEARCH [10]....
[...]
...For 16S rRNA gene sequences, BLAST+, UCLUST, and VSEARCH consensus classifiers perform best for novel taxon classification (Table 2)....
[...]
1,676 citations
1,181 citations
Cites methods from "VSEARCH: a versatile open source to..."
...Reads are filtered for de novo chimeras using UCHIME (8) as implemented by VSEARCH (9) using modified parameters (Text S1)....
[...]
...However, it is possible that the reads would still contain chimeras originating from PCR. Reads are filtered for de novo chimeras using UCHIME (8) as implemented by VSEARCH (9) using modified parameters (Text S1)....
[...]
1,038 citations
References
70,111 citations
"VSEARCH: a versatile open source to..." refers methods in this paper
...This second phase is probably where USEARCH and VSEARCH differ the most, as USEARCH by default presumably performs heuristic seed-and-extend alignment similar to BLAST (Altschul et al., 1997), and only performs optimal alignment when the option fulldp (full dynamic programming) is used....
[...]
43,862 citations
"VSEARCH: a versatile open source to..." refers methods in this paper
...Rognes et al. (2016), PeerJ, DOI 10.7717/peerj.2584 10/22...
[...]
...Merged sequences that could be perfectly aligned to their respective reference sequences (either the entire genome or the specific rRNA region) using BWAMEM (Li & Durbin, 2009) were considered correctly merged....
[...]
28,911 citations
"VSEARCH: a versatile open source to..." refers methods in this paper
...QIIME and UPARSE are both based on USEARCH (Edgar, 2010), a set of tools designed and implemented by Robert C. Edgar, and available at http://drive5.com/usearch/....
[...]
..., 2009), QIIME (Caporaso et al., 2010), and UPARSE (Edgar, 2013) are the most popular....
[...]
...In fact, in QIIME many commands will run fine if an alias or link from usearch to vsearch is made....
[...]
...Several pipelines have been developed for microbiome analysis, among which mothur (Schloss et al., 2009), QIIME (Caporaso et al., 2010), and UPARSE (Edgar, 2013) are the most popular....
[...]
18,256 citations
"VSEARCH: a versatile open source to..." refers methods in this paper
...2 segments 3 segments 4 segments Divergence Noise UC U7 U8 V UC U7 U8 V UC U7 U8 V 97–99% – 89 88 88 89 56 52 52 55 38 33 34 35 i1 79 79 77 85 46 44 43 53 32 27 24 34 i2 64 57 56 77 33 32 31 56 24 20 18 33 i3 48 45 36 72 37 35 29 45 16 17 16 21 i4 29 24 23 65 18 11 13 40 9 9 8 25 i5 27 22 16 53 15 12 12 39 7 8 6 17 m1 83 83 83 81 53 48 48 53 33 29 29 30 m2 73 71 71 72 49 44 44 50 28 22 22 27 m3 66 66 66 68 40 40 39 44 21 20 21 21 m4 55 54 53 57 28 24 23 28 21 18 18 19 m5 44 44 42 48 20 19 18 28 16 14 12 12 95–97% – 100 100 100 100 80 77 76 79 64 60 59 63 i1 100 98 98 100 77 75 72 75 54 55 53 61 i2 96 94 93 99 60 55 55 71 48 44 44 60 i3 86 82 82 95 61 50 52 70 38 36 31 53 i4 75 66 64 95 48 41 39 64 29 29 22 47 i5 64 58 53 86 37 32 25 60 24 19 19 46 m1 99 99 99 99 76 73 73 76 60 57 57 60 m2 98 97 97 97 71 69 69 71 50 48 46 48 m3 93 94 94 96 63 61 61 64 41 41 41 42 m4 92 92 90 93 56 55 54 57 39 39 37 41 m5 86 86 85 86 53 51 51 56 35 35 34 34 90–95% – 100 100 100 100 93 93 93 93 88 88 88 86 i1 100 100 100 100 88 88 87 91 86 86 87 88 i2 99 97 99 99 83 79 78 88 74 72 72 84 i3 100 100 100 100 79 76 75 88 74 69 70 82 i4 99 94 96 99 80 71 72 84 66 62 61 79 i5 95 84 86 99 74 65 65 88 55 48 48 71 m1 100 100 100 100 89 89 89 92 87 87 86 85 m2 100 100 100 100 87 87 87 89 78 78 78 79 m3 100 99 99 100 86 86 86 89 76 76 78 80 m4 100 100 100 100 82 82 84 83 73 73 72 78 m5 99 98 98 99 82 81 82 84 75 73 75 79 dataset, while none of the programs work well with the SILVA dataset....
[...]
...All datasets used were small enough to fit comfortably in the memory allocated to a 32-bit process....
[...]
...We evaluated the chimera detection accuracy of VSEARCH and USEARCH in two ways, first using a method similar to that performed for UCHIME, and then using a new chimera simulation procedure based on sequences from Greengenes (DeSantis et al., 2006) and SILVA (Quast et al., 2013) sequences....
[...]
...Next, we tested reference-based (uchime_ref ) and de novo (uchime_denovo) chimera detection using sequences from the 2011 version of Greengenes downloaded from http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/ and from version 106 (May 2011) of the SILVA database downloaded from https://www.arb-silva.de/no_ cache/download/archive/release_106/Exports/....
[...]
...5 and 6 show that de novo chimera detection performs better than reference-based detection, with the SILVA dataset in particular, but it does of course depend on the reference database used....
[...]
17,350 citations
"VSEARCH: a versatile open source to..." refers methods in this paper
...Several pipelines have been developed for microbiome analysis, among which mothur (Schloss et al., 2009), QIIME (Caporaso et al., 2010), and UPARSE (Edgar, 2013) are the most popular....
[...]