inGAP-sv protocols

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chevron_left Deletion detection Insertion detection Comparative genome visualization Inversion detection CNV detection chevron_right
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inGAP-sv specifications

Information


Unique identifier OMICS_00319
Name inGAP-sv
Alternative name inGAP
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

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Publication for inGAP-sv

inGAP-sv in pipelines

 (4)
2016
PMCID: 4938650
PMID: 27172215
DOI: 10.1534/g3.116.029504

[…] breakpoints were analyzed using polymerase chain reaction (pcr)-based sanger sequencing with the primers listed in supplemental material, file s1. inversions were displayed using rcircos () and ingap-sv ()., snpeff v4.0e () was used to annotate the identified snps based on the rnor5.0.74 rat assembly. our previously sequenced individual genome of the ahr sibling species, r. rattus, was also […]

2016
PMCID: 5114782
PMID: 27855707
DOI: 10.1186/s13059-016-1094-x

[…] of these transcripts before and after svm filtration, respectively. the node number and the ratio of positive nodes in the components of each graph were calculated., to assess the performance of ingap-cdg when identifying orthologous genes for phylogenetic analysis, two 100-bp paired-end rna-seq datasets were downloaded from the ncbi database (sra accession numbers of srr3151756 […]

2012
PMCID: 3430611
PMID: 22952860
DOI: 10.1371/journal.pone.0044030

[…] ismatch = 1) for further base calling. genome analyzer pipeline sequence data was then analyzed using mapping and assembly with quality (maq) and integrative next-generation genome analysis pipeline (ingap) sequence analysis software to identify single nucleotide polymorphisms, insertions, and deletions for the sequenced genomes compared to the s. typhimurium str. lt2 genome reference sequence (nc […]

2009
PMCID: 2770529
PMID: 19832984
DOI: 10.1186/1471-2164-10-475

[…] detailed multiple alignment by clustalw []., last, whole genome mapping and visualization were applied to all 4 meiotic products near the snps. we developed a whole genome visualization tool, named ingap to display all homology exchange among meiotic products. the manuscript has been submitted (ji qi, fangqing zhao, anne buboltz and stephan c. schuster) and the software is available online at , […]


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inGAP-sv in publications

 (92)
PMCID: 5893557
PMID: 29636466
DOI: 10.1038/s41467-018-03640-y

[…] jnk-inhibiting peptide composed of d-amino acids for the treatment of stroke, inflammation, severe inner ear disorders and acute sensorineural hearing loss; the islet neogenesis-associated protein (ingap) peptide (exsulin corporation) for islet beta cell neogenesis and improvement in glycemic control in type 1 diabetic patients, and azx100 (capstone therapeutics), a peptide derived from hsp20 […]

PMCID: 5841313
PMID: 29515199
DOI: 10.1038/s41598-018-22321-w

[…] in carrier mobility of algan/gan hfet devices with increasing ion fluence. titov et al. reported that mev o, li, and si ions lead to a decrease in the free-carrier concentration of gan and ingap materials. as the application of gan-based devices in the space and reactor fields continues to grow and their size has been ceaselessly minimized, more information regarding defects […]

PMCID: 5812990
PMID: 29445168
DOI: 10.1038/s41467-018-03103-4

[…] much lower (~800–1200 nm) than photon energies in the maximum of the sunlight spectrum (~500–600 nm). while other photovoltaic materials with much higher energy conversion efficiencies such as ingap exist for this spectral range, they are, unfortunately, extremely expensive. therefore, they are often used in combination with solar light concentrators that allow collecting light from larger […]

PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] we will also explain the core algorithm of each variant caller and, if applicable, highlight the strengths and caveats. germline-only callers, such as gatk unifiedgenotyper/haplotypecaller, ingap, and maq , , , are not included in this review. although unifiedgenotyper and haplotypecaller have been used for somatic variant calling, their core algorithms are not designed for this task […]

PMCID: 5719756
PMID: 29212471
DOI: 10.1186/s12866-017-1138-8

[…] grey jiaobai of the longjiao 2# variety were deposited in genbank under accession number srr5889164. genome analysis tk (version 1.6) and sam tools 1.9 were used to identify the snps and indels. ingap-sv was used to identify the structure variations []., genomic dna of the fungi was extracted by the ctab method []. fragments were amplified by a standard pcr procedure with primers […]


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inGAP-sv institution(s)
Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China

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