Spanki protocols

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chevron_left Alternative splicing events identification Read simulation chevron_right
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Spanki specifications

Information


Unique identifier OMICS_01414
Name Spanki
Alternative name Splicing analysis kit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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http://www.cbcb.umd.edu/software/spanki/

Publication for Splicing analysis kit

Spanki in pipelines

 (3)
2017
PMCID: 5417610
PMID: 28472135
DOI: 10.1371/journal.pone.0176768

[…] format. fragments per kilobase of transcript per million (fpkm) values were calculated using cufflinks version v2.0.2 []. for analyses of mouse genes, transcript splice forms were identified using spanki version 0.4.0 []. genes were annotated and gene counts generated using the intersectbed application from bedtools version 2.18.2 []. reads per kilobase of transcript per million (rpkm) values […]

2017
PMCID: 5423905
PMID: 28539927
DOI: 10.3389/fpls.2017.00694

[…] pasa 2.0 () to remove redundancy. we further filtered splice isoforms by requiring: (1) splice junctions within the transcripts were confirmed with splicing entropy score above 2 calculated using spanki v0.5.0 with default parameters (); (2) retained introns had a minimum median read coverage of 10 over a minimum of 90% of the intron length and a minimal intron retention percentage of 10% (); […]

2017
PMCID: 5763373
PMID: 29353941
DOI: 10.1111/rssc.12213

[…] as discussed in müller et al. ()., a set of simulation studies is used to benchmark the proposed methodology by using synthetic rna‐seq reads from the drosophila melanogaster transcriptome. the spanki software (sturgill et al., ) is used for this. in addition to the simulated data study we also perform a comparison for two real data sets: a low and high coverage sequencing experiment using […]


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Spanki in publications

 (5)
PMCID: 5423905
PMID: 28539927
DOI: 10.3389/fpls.2017.00694

[…] pasa 2.0 () to remove redundancy. we further filtered splice isoforms by requiring: (1) splice junctions within the transcripts were confirmed with splicing entropy score above 2 calculated using spanki v0.5.0 with default parameters (); (2) retained introns had a minimum median read coverage of 10 over a minimum of 90% of the intron length and a minimal intron retention percentage of 10% (); […]

PMCID: 5763373
PMID: 29353941
DOI: 10.1111/rssc.12213

[…] as discussed in müller et al. ()., a set of simulation studies is used to benchmark the proposed methodology by using synthetic rna‐seq reads from the drosophila melanogaster transcriptome. the spanki software (sturgill et al., ) is used for this. in addition to the simulated data study we also perform a comparison for two real data sets: a low and high coverage sequencing experiment using […]

PMCID: 4802181
PMID: 26997247
DOI: 10.1038/ncomms10966

[…] between the two methods (). complete gene-level output from each program is provided in ., splicing was analysed by multiple complementary approaches. we used the splicing analysis toolkit (spanki) v.0.4.3 (ref. ) to quantify splice junction coverage from alignment files, and to quantify proportion spliced in for splicing events. the astalavista tool was used to characterize events […]

PMCID: 4683657
PMID: 26511498
DOI: 10.1534/g3.115.023721

[…] () and bowtie2 (2.1.0) () with the following settings: -g 1–library-type fr-firststrand –g. the output bam files were then indexed and sorted by samtools (0.1.19) (li et al. 2009) and used in spanki (0.4.3) () and miso (0.5.2) () for alternative splicing analysis. for spanki analysis: (1) we ran with the built-in command spankijunc from spanki with “-m all” option; (2) curated junctions […]

PMCID: 4289277
PMID: 25262759
DOI: 10.1186/gb-2014-15-8-r70

[…] was used to account for the random hexamer-based bias. for the results presented in this study, we used fpkm >1 as a cutoff for gene expression []., we analyzed sex-specific splicing events using spanki 0.4.0 (splicing analysis kit) []. we used the quickjunc utility within spanki, with alignment files generated by tophat as input, to quantify splice junction coverage, requiring an anchor size […]


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Spanki institution(s)
National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, MD, USA

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