Graphmap index align 0.5.2
This App runs Graphmap (version 0.5.2):
A highly sensitive and accurate mapper for long, error-prone reads
Graphmap requires the following:
- reference genome in fasta format (may be gzipped) (an index (.gmidx) of the reference genome may be provided as well if one has already been generated)
- long reads in fastq or fasta format (may be gzipped)
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Graphmap
- Reference genome fasta file
- Oxford Nanopore reads file
Parameters Used in App
- In the Input section choose the reference genome fasta input file: 'GCF_000146045.2_R64_genomic.fna.gz'.
- In the Input section select the Oxford Nanopore reads input file: 'fastq_runid_01f68662d08b0a5d21077bf590c4c497b9092ef0_0.fastq'.
- In the Input section select 'FASTQ' drop-down menu.
- In the Output section name the output file 'testout.sam'
- All remaining parameters may be left as default.
- This is the index file of the genome generated by the app. This file may be used in future analyses in place of the reference genome fasta file.
- This is the alignment file generated by the app. Following the above parameters it will be named 'testout.sam'.