NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes.
The explosion of bioinformatics technologies in the form of next generation sequencing (NGS) has facilitated a massive influx of genomics data in the form of short reads. Short read mapping is therefore a fundamental component of next generation sequencing pipelines which routinely match these short...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC4731464?pdf=render |
| _version_ | 1819231808841056256 |
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| author | Gabriel A Al-Ghalith Emmanuel Montassier Henry N Ward Dan Knights |
| author_facet | Gabriel A Al-Ghalith Emmanuel Montassier Henry N Ward Dan Knights |
| author_sort | Gabriel A Al-Ghalith |
| collection | DOAJ |
| description | The explosion of bioinformatics technologies in the form of next generation sequencing (NGS) has facilitated a massive influx of genomics data in the form of short reads. Short read mapping is therefore a fundamental component of next generation sequencing pipelines which routinely match these short reads against reference genomes for contig assembly. However, such techniques have seldom been applied to microbial marker gene sequencing studies, which have mostly relied on novel heuristic approaches. We propose NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS, or NINJA for short), a fast and highly accurate novel method enabling reference-based marker gene matching (picking Operational Taxonomic Units, or OTUs). NINJA takes advantage of the Burrows-Wheeler (BW) alignment using an artificial reference chromosome composed of concatenated reference sequences, the "concatesome," as the BW input. Other features include automatic support for paired-end reads with arbitrary insert sizes. NINJA is also free and open source and implements several pre-filtering methods that elicit substantial speedup when coupled with existing tools. We applied NINJA to several published microbiome studies, obtaining accuracy similar to or better than previous reference-based OTU-picking methods while achieving an order of magnitude or more speedup and using a fraction of the memory footprint. NINJA is a complete pipeline that takes a FASTA-formatted input file and outputs a QIIME-formatted taxonomy-annotated BIOM file for an entire MiSeq run of human gut microbiome 16S genes in under 10 minutes on a dual-core laptop. |
| first_indexed | 2024-12-23T11:50:51Z |
| format | Article |
| id | doaj.art-d276b358482a4dd39a36a68c353e31e0 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-23T11:50:51Z |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-d276b358482a4dd39a36a68c353e31e02022-12-21T17:48:13ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582016-01-01121e100465810.1371/journal.pcbi.1004658NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes.Gabriel A Al-GhalithEmmanuel MontassierHenry N WardDan KnightsThe explosion of bioinformatics technologies in the form of next generation sequencing (NGS) has facilitated a massive influx of genomics data in the form of short reads. Short read mapping is therefore a fundamental component of next generation sequencing pipelines which routinely match these short reads against reference genomes for contig assembly. However, such techniques have seldom been applied to microbial marker gene sequencing studies, which have mostly relied on novel heuristic approaches. We propose NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS, or NINJA for short), a fast and highly accurate novel method enabling reference-based marker gene matching (picking Operational Taxonomic Units, or OTUs). NINJA takes advantage of the Burrows-Wheeler (BW) alignment using an artificial reference chromosome composed of concatenated reference sequences, the "concatesome," as the BW input. Other features include automatic support for paired-end reads with arbitrary insert sizes. NINJA is also free and open source and implements several pre-filtering methods that elicit substantial speedup when coupled with existing tools. We applied NINJA to several published microbiome studies, obtaining accuracy similar to or better than previous reference-based OTU-picking methods while achieving an order of magnitude or more speedup and using a fraction of the memory footprint. NINJA is a complete pipeline that takes a FASTA-formatted input file and outputs a QIIME-formatted taxonomy-annotated BIOM file for an entire MiSeq run of human gut microbiome 16S genes in under 10 minutes on a dual-core laptop.http://europepmc.org/articles/PMC4731464?pdf=render |
| spellingShingle | Gabriel A Al-Ghalith Emmanuel Montassier Henry N Ward Dan Knights NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes. PLoS Computational Biology |
| title | NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes. |
| title_full | NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes. |
| title_fullStr | NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes. |
| title_full_unstemmed | NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes. |
| title_short | NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes. |
| title_sort | ninja ops fast accurate marker gene alignment using concatenated ribosomes |
| url | http://europepmc.org/articles/PMC4731464?pdf=render |
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