GraphMap - A highly sensitive and accurate mapper for long, error-prone reads

Version: v0.18b Release date: 11 December 2014

Precompiled binary, built on Mint 16 (Ubuntu 13.10) x64. Tested on Mint 17 (Ubuntu 14.04), Ubuntu Server 14.04, Fedora 20 and Gentoo.

Description

GraphMap is a novel mapper targeted at aligning long, error-prone third-generation sequencing data. It can handle Oxford Nanopore data with very high sensitivity and accuracy, and also presents a significant improvement over the state-of-the-art for PacBio read mappers (namely, compared to BLASR and BWA-MEM).

GraphMap was designed for ease-of-use: the default parameters can handle a wide range of read lengths and error profiles. This is an important feature for technologies where the error rates and error profiles can vary widely across sequencing runs. In addition, GraphMap allows users to uniformly map read datasets from disparate technologies with high sensitivity and accuracy. While GraphMap is not runtime optimized for short-read data (e.g. compared to Bowtie2), it provides accurate and typically more sensitive mappings for Illumina and Ion Torrent reads.

Please keep in mind that this is an early development version and we welcome your comments and feedback on GraphMap.

Comparison to other mappers

Comparison statistics will be uploaded soon.

Usage

# Process all reads from a given FASTA/FASTQ file with maximum number of threads:
./graphmap -r escherichia_coli.fa -d reads.fastq -o alignments.sam

# Limit the number of threads to 8, and load reads in batches of 50MB:
./graphmap -t 8 -B 50 -r escherichia_coli.fa -d reads.fastq -o alignments.sam

# Process only the first 1000 reads:
./graphmap -B 0 -n 1000 -r escherichia_coli.fa -d reads.fastq -o alignments.sam

# Process all reads from a given folder.
./graphmap -r escherichia_coli.fa -D reads_folder -O alignments_folder

# Generate only the index.
./graphmap -I -r escherichia_coli.fa

Contact information

For additional information, help and bug reports please send an email to one of the following: ivan.sovic@irb.hr, mile.sikic@fer.hr, nagarajann@gis.a-star.edu.sg