I have fastq files generated using multiplex MinION nanopore sequencing (long reads) on a specific fungus, I employed minimap2, samtools, and freebayes to generate my VCF file. I have two questions:
Which tool should I use to trim reads before minimap2, considering that I need a tool that not only allows me to specify read length but also permits me to specify the read size to trim in the 5' prime?
How can I annotate a VCF file and transform it into a list of genes with specified mutations?
If you have a tutorial, steps, or scripts to address these questions, I would greatly appreciate your assistance. Thank you in advance, and I hope to receive answers to my inquiries!
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emilydolivo5 •
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bbduk.shwithminlen=NN maxlen=NN forcetrimleft=NNoptions. Other trimming programs will likely have similar options (fastpetc).A guide is available: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/
snpEff, VEP and like. VEP Tutorial: http://useast.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html