The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Nanopolish-variants-0.10.2

This App runs Nanopolish (version 0.10.2) to 

  • Detect SNPs and indels with respect to a reference genome.

App Creator

Amanda Cooksey

Quick Start

  • Nanopolish 0.10.2 variants takes the following files as input: 
  • Oxford Nanopore reads in FASTA format 
  • Corresponding FAST5 files
  • Indexed, sorted BAM file of those reads aligned to a reference genome 
  • Reference genome in FASTA format

Test Data

Icon

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

Input File(s)

Use these files from the folder above as example data:

bwa_output_sorted.bam 
bwa_output_sorted.bam.bai 
fastq_runid_01f68662d08b0a5d21077bf590c4c497b9092ef0_0.fastq 
fastq_runid_01f68662d08b0a5d21077bf590c4c497b9092ef0_0.fastq.index 
fastq_runid_01f68662d08b0a5d21077bf590c4c497b9092ef0_0.fastq.index.fai
fastq_runid_01f68662d08b0a5d21077bf590c4c497b9092ef0_0.fastq.index.gzi
fastq_runid_01f68662d08b0a5d21077bf590c4c497b9092ef0_0.fastq.index.readdb
GCF_000240185.1_ASM24018v2_genomic.fna
raw_fast5_subset (FAST5 directory)

 

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.

Window: NC_016845.1:1-5333942

Ploidy: 1

Minimum candidate depth: 2

Leave all other parameters as default.

Output File(s)

With the above parameters Nanopolish variants creates one output file called variants_output.vcf.

Tool Source for App

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