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CSB5 / INC-Seq

INC-Seq: Accurate single molecule reads using nanopore sequencing
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Consensus building for 1D #10

Closed kylacochrane closed 5 years ago

kylacochrane commented 5 years ago

Is it possible to use INC-seq with the NanoPore 1D kits? I used the 1D 16S PCR barcoding kit to generate full length 16S reads.

I run this code (with my demultiplexed fasta file);

$ ./inc-seq.py -i ~/$.fasta -m 1000 -o consensus.fa

And this is the output: ---------- Processing read 1 ---------- Max number of segments found: 0 Consensus construction failed! ---------- Processing read 2 ---------- Max number of segments found: 0 Consensus construction failed! ...etc

Any help would be greatly appreciated. Thanks so much!

lch14forever commented 5 years ago

Hi,

I am afraid that standard 16S full length library will not work. INC-Seq needs tandem repeats in the reads generated using Rolling Circle Amplification.

Regards, Chenhao