I want to ask what is the common approach to do the recalibration of base quality scores for the bioinfomatics analysis of the bacteria and virus WGS data? Based on what I read online, you can use the gold set from the 1000 genomes project for the human genome, but for bacteria and virus genome, can I use this database? if not, is there other database I can use? or I should do the bootstrapping approach described in this link https://learn.gencore.bio.nyu.edu/variant-calling/pre-processing/ ?
As I remember, you could obtain raw-vcf file directly from bam file and create database from SNPs with high coverage from this vcf.
But do you really need this step?
In bacteria and viruses you should obtain fastq with very high coverage and most of them must be with high Q-score (if you do quality-check and trimming right)
Also you could try to get de novo genome assembly of bacteria from your data, get raw SNPs from this assembly and compare them with SNPs from aligning reads on reference data.
Yeah. Usually 40X coverage. OK, I will try the de novo genome assembly approach. Thanks.
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