Section: New Software and Platforms

short read connector

Keywords: Bioinformatics - Genomics - Metagenomics

Scientific Description

Short read connector enables the comparisons of two read sets B and Q. For each read from Q it provides either:

The number of occurrences of each k-mers of the read in the set B (SRC_counter) or A list of reads from B that share enough k-mers with the tested read from B (SRC_linker)

Functional Description

This tool uses a data structure (BBHASH) adapted to the indexing of big data. Short Read Connector works on reads, which are sequencing data from high-throughput sequencers. Once the data is indexed, short read connector makes it possible either to find the similar reads in a dataset or to simply retrieve the approximate number of these similar reads.

• Participants: Pierre Peterlongo, Camille Marchet and Antoine Limasset

• Partner: UPMC

• Contact: Pierre Peterlongo

• URL: https://github.com/pierrepeterlongo/short_read_connector