ngs-preprocess
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fmalmeida
A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
A new tool for long reads quality assessment is now available: * https://github.com/yfukasawa/LongQC The task is to evaluate the tool and compare it with NanoPack and pycoQC in order to...
Consider changing the software used to filter the long reads in order to use a more recent and faster app. Currently, [NanoFilt](https://github.com/wdecoster/nanofilt) is used for the task. The software to...
Assess and consider the change from 'porechop' which is deprecated to porechop_abi which is under maintenance. https://github.com/bonsai-team/Porechop_ABI
Some tools from NanoPack have been replaced for quicker tools as described here: https://github.com/wdecoster/nanopack?tab=readme-ov-file The task would be to update such tools in the pipeline.