Readjoiner statistics

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Readjoiner specifications


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
Source code URL
Maintained Yes



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  • person_outline Stefan Kurtz <>

Publication for Readjoiner

Readjoiner in publications

PMCID: 5331309
PMID: 28293632
DOI: 10.1155/2017/2731385

[…] number of sequences (reads) which require further processing. the generated sequences represent segments from multiple copies of the original genome. an overlap-based assembler, such as sga [] and readjoiner [], finds overlaps between these reads in order to build a string graph which will be the input for the assembly stage. the problem of finding overlaps between each ordered pair of reads […]

PMCID: 4417569
PMID: 25961045
DOI: 10.1155/2015/905261

[…] compact prefix tree in the process of building the targeted data structure., apsp has been used in the overlap stage of the genome assembly process. two important modern assemblers are sga [] and readjoiner []. in sga, the fm index [] is used to solve the problem in an indirect way as follows. the index is constructed for all strings after concatenating them in one string. then the index […]

PMCID: 4066913
PMID: 24999437
DOI: 10.1080/21501203.2014.919967

[…] the quality trimming with a maximum number of two ambiguous nucleotides at the sequence ends allowed., a number of assembly programs were investigated and compared, including open source software, readjoiner (), string graph assembler (sga) (), abyss (), soap denovo () and the commercial software, clc-bio genomics workbench. assemblies were reiterated with different overlap length […]

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

[…] 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 […]

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

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