Incorporating a UBAM to FastQ step to the fastp package

OpenGene / fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

MIT License

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Incorporating a UBAM to FastQ step to the fastp package #161

Open shumbakadzi opened 5 years ago

shumbakadzi commented 5 years ago

Some of our Sequencing Service providers deliver to us paired-end sequence data in UBAM (unaligned) file format containing both forward and reverse reads. Do you think it would be helpful to many users if you included a step that converts the UBAM file to FastQ to the fastp tool? I am new to using Biostars otherwise I would have posted this comment there to find out what other people think about this. Thank you.

sfchen commented 5 years ago

Any other guys want this feature?

Ackia commented 5 years ago

I think this might be a good additional function. For one, working with non-Illumina technologies uBAM is not uncommon. As I am working with datasets that require metadata-attachment I would like this option for that reason alone. Although bigger and bulkier the uBAM format has some benefits.

This post over at BROAD has some good thoughts on the subject https://gatkforums.broadinstitute.org/gatk/discussion/5990/what-is-ubam-and-why-is-it-better-than-fastq-for-storing-unmapped-sequence-data