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eblerjana / pangenie

Pangenome-based genome inference
MIT License
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Can long-reads be use for <reads.fa/fq>？ #10

Open lxxiaoxiaLi opened 2 years ago

lxxiaoxiaLi commented 2 years ago

Hi, Thank you very much for such a nice tool. usage: PanGenie [options] -i <reads.fa/fq> -r -v I fund the paper (https://www.biorxiv.org/content/10.1101/2020.11.11.378133v1）said that ：we propose a new algorithm, PanGenie, that leverages a haplotype-resolved pangenome reference together with k-mer counts from short-read sequencing data to genotype a wide spectrum of genetic variation....

May I ask if the pangenie software can only use short reads? Can long-reads be use for <reads.fa/fq> (such as Nanopore or PacBio reads)? ，What is the advantage over the second generation The genotype of the outfile is the genotype of reads (i.e -i <reads.fa/fq>) that corresponds to the sample, rigth？

Thanks.

eblerjana commented 2 years ago

PanGenie is designed for short reads. Since it uses kmer information from the input reads for genotyping, it is important that the error rate of the sequencing data used is small. So we do not recommend using PacBio or Nanopore reads as input.