python3-pychopper

identify, orient and trim full-length Nanopore cDNA reads

Description

Pychopper v2 is a Python module to identify, orient and trim full-length Nanopore cDNA reads. It is also able to rescue fused reads and provides the script 'pychopper.py'. The general approach of Pychopper v2 is the following:

* Pychopper first identifies alignment hits of the primers across the

length of the sequence. The default method for doing this is using

nhmmscan with the pre-trained strand specific profile HMMs, included

with the package. Alternatively, one can use the edlib backend,

which uses a combination of global and local alignment to identify

the primers within the read.

* After identifying the primer hits by either of the backends, the

reads are divided into segments defined by two consecutive primer

hits. The score of a segment is its length if the configuration of

the flanking primer hits is valid (such as SPP,-VNP for forward reads)

or zero otherwise.

* The segments are assigned to rescued reads using a dynamic programming

algorithm maximizing the sum of used segment scores (hence the amount

of rescued bases). A crucial observation about the algorithm is that

if a segment is included as a rescued read, then the next segment

must be excluded as one of the primer hits defining it was "used

up" by the previous segment. This put constraints on the dynamic

programming graph. The arrows in read define the optimal path for

rescuing two fused reads with the a total score of l1 l3.

A crucial parameter of Pychopper v2 is -q, which determines the stringency of primer alignment (E-value in the case of the pHMM backend). This can be explicitly specified by the user, however by default it is optimized on a random sample of input reads to produce the maximum number of classified reads.

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Homepage

https://github.com/epi2me-labs/pychopper

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