Assemblytics statistics

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Assemblytics specifications

Information


Unique identifier OMICS_11402
Name Assemblytics
Interface Web user interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche, Oxford Nanopore
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Maria ttestad <>

Information


Unique identifier OMICS_11402
Name Assemblytics
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche, Oxford Nanopore
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Maria ttestad <>

Publication for Assemblytics

Assemblytics in publications

 (7)
PMCID: 5821087
PMID: 29463659
DOI: 10.1128/mBio.02275-17

[…] higher level of interhaplotype variation when using this phased assembly. for this analysis, we aligned all haplotigs with their corresponding primary contigs and estimated variations by using assemblytics (, ). assemblytics defines six major categories of structural variations, including insertions and deletions, tandem repeats identified by overlapping alignments and other types […]

PMCID: 5821079
PMID: 29463655
DOI: 10.1128/mBio.01650-17

[…] overlap annotated genes. colors indicate different classes of sv (shown in the key). graphs in panels c and d show size distributions of structural variants from 50 to 10,000 bp identified using assemblytics in haplotigs relative to primary contigs of 12sd80 and 12nc29, respectively. (e) distribution of small variants in and around predicted effectors on primary contigs of 12sd80 and 12nc29. […]

PMCID: 5803254
PMID: 29416032
DOI: 10.1038/s41467-018-03016-2

[…] g representative sequence from col-0 tair10; the kbs-mac-74 specific repeats were then used to search all four assemblies. structural variation between assembled genomes and tair10 were detected with assemblytics based on whole genomes alignments generated with mummer. for sg3/sg3i analysis, the complete genomic region for at4g30720 was blasted against the kbs-mac-74 ontmin round 4 assembly; 50 kb […]

PMCID: 5889714
PMID: 29431738
DOI: 10.1038/nbt.4060

[…] with “mummer -plot-fat” using the 1-to-1 filtered matches. a previously published gm12878 pacbio assembly was aligned as above with mummer v3.23. the resulting alignment files were uploaded to assemblytics to identify structural variants and generate summary figures. versus grch38, the pacbio assembly identified 10,747 structural variants affecting 10.84 mbp, and reported an equal balance […]

PMCID: 5770396
PMID: 29376038
DOI: 10.3389/fcimb.2017.00539

[…] (sift 4g) (kumar et al., ). predictions with a score <0.05 were considered significant., structural variations (svs, ranging 1–10,000 bp) present in h112 but absent in h54 were identified using assemblytics (nattestad and schatz, ). briefly, genome assemblies were aligned against the reference genome m. tuberculosis h37rv (nc_000962.3) using nucmer with –minmatch 100 and –mincluster 500. […]


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Assemblytics institution(s)
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
Assemblytics funding source(s)
NSF [DBI-1350041]; NHGRI [R01-HG006677]

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