Nanopolish vcf2fasta 0.10.2

This App runs Nanopolish (version 0.10.2) to

Write a new genome sequence by introducing variants from the input files.

App Creator

Amanda Cooksey

Quick Start

Nanopolish vcf2fasta 0.10.2 takes vcf files generated with Nanopolish variants --consensus
Draft sequence in FASTA format

Resources: https://github.com/jts/nanopolish and https://media.readthedocs.org/pdf/nanopolish/latest/nanopolish.pdf

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> nanopolish -> vcf2fasta

Input File(s)

Use the variants_output.vcf and GCF_000240185.1_ASM24018v2_genomic_contig1.fna files as input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the section below.

Leave all parameters as default.

Output File(s)

Nanopolish vcf2fasta will generate and output file (as the user named it) the looks like polished_contig1.fasta in the example folder.

Tool Source for App

https://github.com/jts/nanopolish