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zellerlab / stag

A hierarchical taxonomic classifier for metagenomic sequences
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fastq input #2

Closed AlessioMilanese closed 4 years ago

AlessioMilanese commented 4 years ago

For now the alignment script (align.py) works only with fasta file, would be good to be able to align also fastq files (and ignore the quality score).

AlessioMilanese commented 4 years ago

The original idea for this was to be able to classify 16S amplicon data directly. The issue is that there are anyway two reads (paired-end reads have forward and reverse) and you might want to do some filtering and quality control. Hence, we will not add the possibility (at least at the moment) to work on fastq files.