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Meerkat specifications


Unique identifier OMICS_06976
Name Meerkat
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for Meerkat

Meerkat citations


Tracking the genome wide outcomes of a transposable element burst over decades of amplification

Proc Natl Acad Sci U S A
PMCID: 5724284
PMID: 29158416
DOI: 10.1073/pnas.1716459114

[…] as a reference to compare EG4 and likewise A123 assembly was used to discover variants in A119. Read-mapping approaches involved the use of BreakDancer v 1.1.2_2013_03_08 (), Pindel v 0.2.4o (), and Meerkat v 0.175 (), which utilize paired-read information, detection of splits within individual read alignments, and a combination of read pair and split read methods, respectively. RelocaTE was also […]


Genomic analysis of oesophageal squamous cell carcinoma identifies alcohol drinking related mutation signature and genomic alterations

Nat Commun
PMCID: 5477513
PMID: 28548104
DOI: 10.1038/ncomms15290

[…] alue <0.25. For the arm-level analysis, chromosomal arms were considered to be altered if at least 66% of the arm (all_thresholded.by_genes.txt file from the GISTIC output) was lost or gained.We used Meerkat and Delly2 (ref. ) to detect somatic SVs. Since the mean insert size is <300 bp and our WGS data are 150 bp paired-end reads, we first truncated the reads to 100 bp to avoid overlapping of the […]


Integrated genomic and molecular characterization of cervical cancer

PMCID: 5354998
PMID: 28112728
DOI: 10.1038/nature21386

[…] uctural variations in WGS data, 50 low-pass WGS and 19 high-pass WGS samples were analyzed. Detection of structural variations in low-pass WGS data was performed using two algorithms, BreakDancer and Meerkat, with a requirement for at least two discordant read pairs supporting each event and at least one read covering the breakpoint junction. High-pass WGS data were analyzed to detect somatic stru […]


Integrated genomic characterization of oesophageal carcinoma

PMCID: 5651175
PMID: 28052061
DOI: 10.1038/nature20805

[…] WA alignment (to hg19) was used to generate BAM files as previously described (supplementary S3.6 in ref. ). Detection of structural rearrangements was performed using two algorithms, BreakDancer and Meerkat. The set of structural variant calls from each tumour sample was filtered by the calls from its matched normal DNA to remove germline variants. Data were then re-examined using the Meerkat alg […]


Computational characterisation of cancer molecular profiles derived using next generation sequencing

PMCID: 4322529
PMID: 25691827
DOI: 10.5114/wo.2014.47137

[…] []. Several methods for detecting somatic mutations are currently in use, such as MuTect [], Strelka [], and VarScan 2 [] for SNV detection or BIC-Seq [], APOLLOH [], CoNIEFER [], BreakDancer [], and Meerkat [] for CNA or SV detection. Most methods for somatic mutation detection take into account only part of the possible source of errors; therefore, running different methods simultaneously is adv […]

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Meerkat institution(s)
Center for Biomedical Informatics, Harvard Medical School, Boston, MA, USA

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