Nanopolish-index-0.10.2
Nanopolish-index-0.10.2
This App runs Nanopolish (version 0.10.2) to
- Build an index mapping from basecalled reads to the signals measured by the sequencer.
- This app should be run if your data were basecalled with Albacore 2.0 or later. If your data were basecalled with Albacore 1.2 or earlier you should use Nanopolish_extract instead.
App Creator
Amanda Cooksey
Quick Start
- Nanopolish 0.10.2 takes a directory FAST5 files and basecalled reads in FASTA or FASTQ format as input.
- 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 -> index
Input File(s)
Use the the following files from the Nanopolish index directory above for an example run:
fast5_files directory
reads.fa
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 index will produce the following files:
reads.fa.index
reads.fa.indexfai
reads.fa.index.gzi
reads.fa.index.readdb