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Old 05-30-2018, 12:44 AM   #1
francescawinter212
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Hi everyone,

I have got data for two regions of the 16S gene using Illumina MiSeq 2x250bp protocol but I am missing a large chunk of sequence from between the two reads. So there is no overlap. These reads have been taken from a mixed population. I don't want to have to analyse the two reads from a pair individually. Is there any way of linking the two reads from a pair together for data analysis? And what programs would everyone recommend for data analysis of 16S sequence for taxonomic assignment? I've been thinking about using QIIME or PANDAseq.

Also, would it make sense to generate a reference library containing just the sequence 250bp downstream of the two primer sites? The problem here might be that the reads are never 250bp long due to drop off in quality.

Last edited by francescawinter212; 05-31-2018 at 06:57 AM.
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Old 05-31-2018, 04:12 AM   #2
colindaven
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Yep, have a look at Flash or bbmerge from the bbmap package to merge R1 and R2 reads.
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Old 05-31-2018, 04:19 AM   #3
GenoMax
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While bbmerge can be used to merge the reads in this case it will require the reference sequence since OP says:

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I am missing a large chunk of sequence from between the two reads
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