Readjoiner statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Readjoiner
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Protocols

Readjoiner specifications

Information


Unique identifier OMICS_12867
Name Readjoiner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format Readjoiner supports the input formats FastQ and Fasta.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Version 1.2
Stability Stable
Requirements
GenomeTools
Source code URL http://genometools.org/pub/genometools-unstable.tar.gz
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Stefan Kurtz

Publication for Readjoiner

Readjoiner citations

 (3)
call_split

SeedsGraph: an efficient assembler for next generation sequencing data

2015
BMC Med Genomics
PMCID: 4460749
PMID: 26044652
DOI: 10.1186/1755-8794-8-S2-S13
call_split See protocol

[…] arge genomes. There are many typical OLC software programs, such as Newbler [], Celera Assembler [], Arachne [] and so forth. Besides these, there are string graph-based assemblers such as SGA [] and Readjoiner [], which take advantage of the FM-index and are derived from the compressed Burrows-Wheeler transform. The bottleneck of OLC methods is the computation of pairwise suffix-prefix alignment […]

library_books

A Practical and Scalable Tool to Find Overlaps between Sequences

2015
Biomed Res Int
PMCID: 4417569
PMID: 25961045
DOI: 10.1155/2015/905261

[…] chine A. It is used to evaluate SOF time and space requirements when limited resources are available.An AWS instance with 16 cores to evaluate the parallelization of our solution and compare SOF with Readjoiner. We refer to it as machine B. It is used to evaluate SOF time and space requirements when dealing with large data sets. […]

library_books

Data compression for sequencing data

2013
PMCID: 3868316
PMID: 24252160
DOI: 10.1186/1748-7188-8-25

[…] ome reads using 54 GB of memory. This was achieved thanks to a compressed data structure, the FM-index [], which will be mentioned also later. Interestingly, another practical string graph assembler, Readjoiner [], which can process 115 Gbp short reads dataset in 52 GB of RAM, does not make use of compressed data structures, but its space effectiveness comes from an ingenious partitioning approach […]


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Readjoiner institution(s)
Center for Bioinformatics, University of Hamburg, Hamburg, Germany

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