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better sequencing #63

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Koeng101 wants to merge 1 commit into main from betterSequencing

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Koeng101 commented Feb 13, 2024

this implements functionality for handling sequencing data better.

First, nanopore sequences are dual barcoded, and if they have a well, they are filtered out. The dual barcoded wells are then megamashed. All this data is saved to a different fastq file.
This outputs reads (fastq) and a wellsToTemplate csv file.
Those two can be used as an input to generate pileup files for each template.

Pseudo-code would be:

SequenceAnalyze(reads, templateMap, primerMap) (filteredReads, wellsToTemplate)
GeneratePileup(filteredReads, wellsToTemplate) map[well]pileup


          add some better sequencing utils

d1e8f39

Owner Author

Koeng101 commented Feb 14, 2024

merged with #60

Koeng101 closed this

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