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AlignGraph specifications


Unique identifier OMICS_09047
Name AlignGraph
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Paired-end DNA reads in FASTA format, de novo contigs or scaffolds assembled by any de novo DNA-seq assembler, reference genome from a closely related species
Operating system Unix/Linux
License Artistic License version 2.0
Computer skills Advanced
Stability Stable
Aligners Bowtie, BLAT
Maintained Yes


No version available



  • person_outline Thomas Girke <>

Publication for AlignGraph

AlignGraph citations


A hybrid reference guided de novo assembly approach for generating Cyclospora mitochondrion genomes

PMCID: 5891936
PMID: 29643938
DOI: 10.1186/s13099-018-0242-0

[…] by assembling overlapping reads. a contiguous new assembly was generated as a result of significantly greater depth of sequencing thus avoiding gaps and the formation of multiple contigs. tools like aligngraph [] extend the use of paired-end sequencing reads to map to a closely related reference genome and creating contiguous or scaffolded assembly. schneeberger et al. [] used a hybrid approach […]


Draft Genome Sequence of USA100 Methicillin Resistant Staphylococcus aureus Strain 209

PMCID: 5754489
PMID: 29301880
DOI: 10.1128/genomeA.01399-17
call_split See protocol

[…] excluded, which resulted in 15 contigs with a combined total of 2,769,008 bp (n50, 324,561 bp) and with a g+c content of 32.72%. the largest contig was 753,539 bp long. contigs were extended using aligngraph, an algorithm for secondary de novo genome assembly, by aligning contigs and initial raw sequences to closely related references (). s. aureus n315 was identified as the closest related […]


Draft Genome Sequence of the Mucoid Pseudomonas aeruginosa Clinical Isolate PA34

PMCID: 5690347
PMID: 29146840
DOI: 10.1128/genomeA.01307-17

[…] cp012066, cp002496, cp007147, nc_011770, cp014948, and cp007399). specifically, an initial de novo assembly was generated using spades 3.10 and improved with ragout to inform contig order and aligngraph to close the gaps between scaffolds (). the assembly was improved through iterative remapping of the reads to the assembly using icorn2 to correct amplification errors and indel assembly […]


Reference guided de novo assembly approach improves genome reconstruction for related species

PMCID: 5681816
PMID: 29126390
DOI: 10.1186/s12859-017-1911-6

[…] may be improved by running it iteratively, in which the assembled genome is used as a reference in a next round of reference-guided de novo assembly [] or in other reference guided algorithms like aligngraph []., besides all these, our study shows that longer assemblies or assemblies with a high n50 or ng50 are not always the best assemblies (see fig. ). contigs or scaffolds maybe wrongly […]


Pathogenicity Locus, Core Genome, and Accessory Gene Contributions to Clostridium difficile Virulence

PMCID: 5550754
PMID: 28790208
DOI: 10.1128/mBio.00885-17

[…] reads was performed using trimmomatic version 0.35 (). trimmed reads were assembled into contigs using the short read assembler spades (v.3.6.1) (), and secondary scaffolding was performed with aligngraph using published c. difficile reference sequences to guide the assembly (). quality assessment of finished assemblies was performed using quast (v.4.4) (). the assemblies […]


Genome Sequencing and Analysis of the Postharvest Fungus Penicillium expansum R21

PMCID: 5313603
PMID: 28209811
DOI: 10.1128/genomeA.01516-16

[…] on all data using soapdenovo v2.04 ( with 59 k-mer after a k-mer sweep evaluation. the contigs was then extended using reference guided assembly improvement tool aligngraph ( with one p. expansum reference genome (asm76974v1) and scaffolding by sspace-standard (). the final assembly consisted of 573 contigs, with an n50 […]

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AlignGraph institution(s)
Department of Computer Science and Engineering; Department of Botany and Plant Sciences, University of California, Riverside, CA, USA

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