BatAlign statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

Associated diseases

BatAlign specifications


Unique identifier OMICS_09206
Name BatAlign
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Fastq/fasta file
Input format FASTA,FASTQ
Output data SAM-format
Output format SAM
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Wing Kin Sung <>

Publication for BatAlign

BatAlign in publications

PMCID: 5846869
PMID: 29568413
DOI: 10.1007/s13258-017-0621-9

[…] furthermore, tools that were developed after the previous review papers or those that have not been widely compared previously in review papers, were also selected and included batalign (lim et al. ) showing higher sensitivity and specificity than bwa–mem and bowtie 2 when processing short reads with structural variants, bwa–pssm (kerpedjiev et al. ) outperforming […]

PMCID: 5100849
PMID: 27613752
DOI: 10.1534/g3.116.034488

[…] gsnap () into our study, despite the fact that this tool was designed for aligning rna-seq data (i.e., alignments with large gaps to allow for spliced introns). we also aimed to include gem (), batalign (), stampy (), and soap2 () into our study but were not able to run these tools on our computational infrastructure (mac pro; batalign: did not respond, gem: compilation failed, stampy: […]

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BatAlign institution(s)
Department of Computer Science, National University of Singapore, Singapore; Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, (CeLS), Singapore; Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore; UAE University, Al Ain, UAE
BatAlign funding source(s)
Supported by the MOEs AcRF Tier 2 Funding [R-252-000-444-112, in part].

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