How are SRC / Simka / Commet (/ Compareads) related?

GATB / short_read_connector

Short Read Connector (SRC)

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How are SRC / Simka / Commet (/ Compareads) related? #1

Closed rchikhi closed 8 years ago

pierrepeterlongo commented 8 years ago

Commet is an important update of compareads (new code, new IOs, binary operations between results) For the others:

(with "scales up" meaning scaling up a project as large as the whole Tara ocean dataset for instance)

rchikhi commented 8 years ago

nice summary! what does "linked similarities" mean?

genscale-admin commented 8 years ago

"linked similarities" denotes the ability of the program to output the similar sequences.

Commet provides the similarity between a read and a read set. "This read (provided) is similar to at least one read (not provided) from this read set"
- SRC_linker provides the identifiers of similar reads.
- Simka does not provide any information about similar sequences, instead it provides measures.

rchikhi commented 8 years ago

i see! thanks for the clarification. I think you could call that "X-vs-Y similarity", with values being "read-vs-read similarity", "read-vs-dataset similarity" and "dataset-vs-dataset similarity", as you already did in the graphic.