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GATB / minia

Minia is a short-read assembler based on a de Bruijn graph
https://gatb.inria.fr/software/minia
GNU Affero General Public License v3.0
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Paired-end read support #2

Closed mictadlo closed 7 years ago

mictadlo commented 8 years ago

Hi, Any plans to implement paired-end read support? Have you ever tried Flash or shuffleReadsfasta.pl from Velvet?

Thank you in advance.

Mic

tseemann commented 8 years ago

@mictadlo shuffleReads just interleaves R1 and R2. FLASH overlaps them into single end reads where possible. You should probably use FLASH before using any assembler which only supports SE reads.

rchikhi commented 7 years ago

Hi, indeed, as per the manual: "Giving paired or mate-pairs reads as input is OK, but keep in mind that Minia won't use pairing information. " Pairing is used when scaffolding. You may use the following pipeline that combines Minia with the BESST scaffolder: https://github.com/GATB/gatb-minia-pipeline