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-eventalign-0.10.2

This App runs Nanopolish (version 0.10.2) to 

  • Align signal-level events to k-mers of a reference genome.

App Creator

Amanda Cooksey

Quick Start

  • Nanopolish 0.10.2 eventalign takes the following files as input: 
  • Oxford Nanopore reads in FASTA/Q format (basecalled with Albacore 2.0 or later)
  • Index files (4) generated by Nanopolish index 
  • Indexed, sorted BAM file of 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 -> eventalign

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.

Leave all parameters as default.

Output File(s)

With the above parameters Nanopolish eventalign will create the file klebs_eventalign_output.txt 

Tool Source for App

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