wook2014 / alfalfa

A Long Fragment Aligner called ALFALFA

alfalfa

ALFALFA: fast and accurate long read mapper

Rapid evolutions in sequencing technology force read mappers into flexible adaptation to longer reads, changing error models, memory barriers and novel applications. The long read mapper ALFALFA achieves high performance in accurately mapping long (>500bp) single-end and paired-end reads to gigabase-scale reference genomes, while remaining competitive for mapping shorter (>100bp) reads. Its seed-and-extend workflow is underpinned by fast retrieval of super-maximal exact matches from an enhanced sparse suffix array, with flexible parameter tuning to balance performance, memory footprint and accuracy.

Downloads

zip containing current version ALFALFA v0.8 zip ALFALFA v0.8 tarball

Installation

Clone repository

1. optional: install git
2. type git clone git://github.com/readmapping/alfalfa.git
3. change into the folder alfalfa
4. type make

Current version zip file

1. unpack using uncompression program such as 7-zip or using unzip alfalfa-master.zip
2. change into the folder alfalfa-master
3. type make

##specific version tarball or zip-file

1. unpack

• zip: unpack using uncompression program such as 7-zip or using unzip alfalfa-version.zip
• tar: tar xvzf alfalfa-version.tar.gz

2. change into the folder alfalfa-version
3. type make

Usage

Usage and command line parameter information can be found on the web page.