Major release

We are releasing version 2 of the Pychopper analysis tool. The package is available for installation from GitHub and bioconda.

Pychopper v2 is used to identify, orientate and trim full-length nanopore cDNA sequence reads. This update also introduces new functionality to rescue the fused reads that are caused by the failure to observe open pore signal. This version is a complete rewrite and supports two different alignment methods (edlib/parasail and profile HMM search from hmmer). The sequence reads are segmented by their primer alignment hits using a dynamic programming algorithm.

Pychopper v2 can use multiple computer cores to speed up analysis and performs automatic tuning of the alignment stringency parameter to maximise the number of classified reads. Evaluation of 50k reads from a SIRV E0 mix dataset produced using the PCR-cDNA Sequencing Kit (SQK-PCS109) demonstrated good performance using both backend alignment methods. More than 90% of input reads were classified or rescued.

Please note that this is tool is available as-is, with minimal support.