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Old 09-08-2016, 05:32 AM   #1
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Location: Denmark

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Default Collapsed reads vs overlapping paired-end reads !!??

Hello all!


We did a Sequencing of three yeast strains (not s.cerevisiae) and with reference genome available!

Illumnia MiSeq

around 8,5 million reads each way (paired ends)

most reads around 90-120 bp long

high coverage: around 90x

In the trimming /adapter removal step we saw most of our paired end reads have overlaps

R1 ------------------------->
R2 <-----------------------

99% overlapping paired end reads
1% non-overlapping paired end reads


Is it better for the next assembly steps (initial contig building, scaffolding)

-> to only use single-end reads:
Collapse the overlapping paired end reads (99 %) into single end reads (since assemblers can have problems with overlapping paired end reads) and use only this single end reads for the assembly (discard the 1%) ?

-> to only use paired-end reads:
use the overlapping paired end reads (99%) and the non-overlapping paired end reads (1%)?

-> to use a mix: single and paired-end reads:
Collapsed into single end reads (99%) and non-overlapping paired end reads (1%).

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Old 09-08-2016, 05:58 PM   #2
Brian Bushnell
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Location: Walnut Creek, CA

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Posts: 2,696

Cross-posted here.
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assembly, paired-end reads

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