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JustinChu / ntsm

This tools counts the number of specific k-mers within sequence data. The counts can then be compare to other counts to determine to compute the probability that sample are of the same origin to discover incongruent samples or sample swaps.
MIT License
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Hello, I would like to ask whether this software has been evaluated for LOD? #2

Closed jsonProgram closed 2 weeks ago

jsonProgram commented 11 months ago
  1. Mainly wondering if NTSM is suitable for low coverage NGSdata?
  2. In other words, how much depth of NGSdata can it be applied to?
JustinChu commented 7 months ago

Sorry for the late reply. ntsm has been tested on 1x coverage (Illumina) and is generally pretty successful. Due to missing sites however, it will not use the PCA-based heuristic but this should be a problem unless you have thousands of samples.

This depends on the quality of the data, low coverage Nanopore data will need higher coverage for example.