V-Xtractor
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Application data |
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| Created by | Hartmann M, Howes CG, Nilsson RH |
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| Biological application domain(s) | Sequencing, Metagenomics |
| Principal bioinformatics method(s) | Statistical calculation |
| Technology | Any |
| Created at | University of British Columbia |
| Maintained? | Yes |
| Input format(s) | FASTA |
| Output format(s) | FASTA, CSV |
| Programming language(s) | Perl |
| Licence | GPL |
| Operating system(s) | UNIX |
Summary: V-Xtractor uses Hidden Markov Models to locate, verify, and extract defined hypervariable sequence segments (V1-V9) from bacterial, archaeal, and fungal small-subunit rRNA sequences.
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Description
Next-generation sequencing technologies are powerful approaches to perform in-depth surveys of highly diverse microbial communities in various environments. Such surveys require processing sequence reads to extract comparable segments of the genetic marker and to eliminate sequencing artefacts. V-Xtractor is a Perl-based, high-throughput software tool that locates, verifies, and extracts defined segments of sequence information from bacterial, archaeal, and fungal small-subunit rRNA gene sequence datasets. Hidden Markov Models are used to detect the conserved boundaries of each hypervariable region of the gene and to extract the interjacent sequence information. With an overall detection efficiency of 99.6% and an extremely low susceptibility to false-positives (0.0004%), this tool enables rapid processing of high-throughput sequencing reads, improves reliability of the data, and facilitates quality control and subsequent analysis in community assays.
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