Data from: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W

Date Published: June 12, 2015

DOI: http://dx.doi.org/10.5061/dryad.54v2q.2

 

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Title Script for extracting DNA sequences flanked by MiFish primer-match regions.
Downloaded 103 times
Description For each of the primer pair, the region with the smallest hamming distance is found in each DNA sequence. If the smallest hamming distance is larger than 3, such sequences are ignored because existence of indels or many mutations is assumed in primer-match regions. For those ignored sequences, manual extraction needs to be conducted afterwards.
Download README.txt (800 bytes)
Download hamming_match.rb (1.153 Kb)
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Title Analytical pipeline for DNA sequences amplified by MiFish primers
Downloaded 143 times
Description The MiFish pipeline works on the Linux/Unix environment. In the first step, the pipeline conducts quality-filtering of the MiFish sequence reads, including Phred score-based low-quality tail-trimming, length filtering, deletion of N base-containing reads, paired-end read assembly, and primer sequences removal. The fasta files of the reads that passed through these quality check are generated. As the next step, the pipeline performs sequence similarity-based species-assignment and the generation of a species by read-count table. This tab-spaced table provides species diversity information detected from the MiFish PCR meta-barcoding analysis of environmental DNAs.
Download MiFish_pipeline.zip (26.85 Kb)
Download README.txt (3.797 Kb)
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When using this data, please cite the original publication:

Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society Open Science 2(7): 150088. http://dx.doi.org/10.1098/rsos.150088

Additionally, please cite the Dryad data package:

Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W (2015) Data from: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.54v2q.2
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