Hi For microbiome study I used nanopore sequencing. The reads were then aligned using LAST tool. The file was then opened in samtools and was processed for variant calling. I want to check the abundance of bacterial community through my reads. 1. So this should be done after variant calling and before making consensus, right? 2. If yes, then how can I know the abundance of each read or community from .vcf file generated after variant calling? 3. Is there any way to convert .vcf to .fasta and will that .fasta file will have all sequences that can show me true abundance?
Thank you so much! Regards Renuka Agarwal Graduate student IISER Mohali
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