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shenwei356 / LexicMap

LexicMap: efficient sequence alignment against millions of prokaryotic genomes
https://bioinf.shenwei.me/LexicMap
MIT License
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Does LexicMap gives result with paried end fastq data and abundance score ? #6

Closed arpit20328 closed 1 month ago

arpit20328 commented 1 month ago

I have paired end data out of illumina in fastq format

like file_R1.fastq and file_R2.fastq

Does LexicMap gives result with paried end fastq data and abundance score ?

I have indexed my reference database as per lexicMap protocol

shenwei356 commented 1 month ago

Does LexicMap support short reads?

LexicMap is mainly designed for sequence alignment with a small number of queries (gene/plasmid/virus/phage sequences) longer than 200 bp by default.

Dear @arpit20328, LexicMap is not designed for paired-end short reads. And no abundance information is outputted.

If you're looking for metagenomic profiling tools, have a look at my KMCP