split concatenated reads from different samples

[mvheetve]

Hi,

I have ONT data (fastq, 1 run) that consists of the same long range amplicons for several samples. PCR primers are identical for all samples, but primers are tailed with sample barcodes. Demultiplexing done by minibar, based on a custom barcode file.

A subset of the data seems to contain reads that are combinations of amplicons from different samples (probably ligated to each other during ligation step of the library prep). Can anyone recommend a strategy to separate these reads into their respective amplicons and bin them in the appropriate sample file.

Regards
mvheetve

[emortiz]

yacrd has a split function, however I don't know if the barcode portion will remain so you can further demultiplex the split reads. I am working as well with amplicons, the coverage is good enough to just discard chimeras (with yacrd as well) instead of trying to split those reads.

[mvheetve]

Hi thanks for answering. Problem solved through Porechop.