Graphmap index align 0.5.2
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
App Creator
Amanda Cooksey
Quick Start
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)
Resources
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Graphmap
Input File(s)
Reference genome fasta file
GCF_000240185.1_ASM24018v2_genomic.fna
Oxford Nanopore reads file
fastq_runid_01f68662d08b0a5d21077bf590c4c497b9092ef0_0.fastq
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.
Output File(s)
GCF_000146045.2_R64_genomic.fna.gmidx
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.
output
This is the alignment file generated by the app. Following the above parameters it will be named 'testout.sam'.