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Paired-end read support #2

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mictadlo opened this issue Aug 17, 2016 · 2 comments
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Paired-end read support #2

mictadlo opened this issue Aug 17, 2016 · 2 comments

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@mictadlo
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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
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tseemann commented Aug 21, 2016 •
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@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
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rchikhi commented Mar 2, 2017

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

@rchikhi rchikhi closed this as completed Mar 2, 2017
@fengcong3 fengcong3 mentioned this issue Jul 16, 2019
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@tseemann @mictadlo @rchikhi