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manuscript-analyses
real-time-phylogenomics @ 68edd33
resequencing
training
visualisation
README.md
USAGE.md
docker-compose.yml
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README.md

live-ID-by-sequencing

A repo for live identification of unknown samples by MinION-sequenced BLAST comparisonss

Parker et al. (2018, in prep) ID-by-sequencing paper

The paper and this code document the rapid-raw-read-reference for ID ('R4ID') approach. This comprises the following steps:

  • A R4ID-training step, in which samples of known origin are MinION-sequenced, or public references downloaded, and used to create labelled BLASTN databases for ID;
  • A R4ID-resequencing step, in which smaples of unknown origin are MinION-sequenced and compared in real-time to the BLASTN R4ID databases to generate lists of read alignments to the R4ID data;
  • A R4ID-visualisation step, in which the lists of BLAST hits are parsed and displayed as a web GUI over a network connection.

Docker

These images are available at https://hub.docker.com/r/lonelyjoeparker/r4ids/

Usage

See USAGE.md

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