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https://github.com/HussainAther/awesome-alternative-splicing

Alternative splicing resource
https://github.com/HussainAther/awesome-alternative-splicing

List: awesome-alternative-splicing

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Alternative splicing resource

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README 

        
# awesome-alternative-splicing

## What is this?

This is a resource for software and information about alternative splicing. [Contributions welcome](https://github.com/hussainather/awesome-alternative-splicing/blob/master/CONTRIBUTING.md)...



## Types of alternative splicing

 - Skipped exon or cassette exon (SE): An exon can be retained or spliced out of the primary transcript.

 - Mutually exclusion exons (MXE): One of two exons is retained in mRNA splicing, but not both.

 - Alternative 5' splice site (A5SS): An alternative 5' splice junction (donor site) is used that changes the 3' boundary of the upstream exon.

 - Alternative 3' splice site (A3SS): An alternative 3' splice junction (acceptor site) is used that changes the 5' boundary of the downstream exon.

 - Retained intron (RI): A sequence may be spliced out as an intron or retained, and there are no flanking introns.



![Types of alternative splicing](images/altsplicetypes.jpeg) 



Source: http://rnaseq-mats.sourceforge.net/rmats3.0.9/



## Software

+ [ALEXA-Seq](http://www.alexaplatform.org/alexa_seq/) - alternative expression analysis by massively parallel sequencing.

+ [AltAnalyze](http://www.altanalyze.org/) - analyze alternative splicing from single-cell and RNA-Seq data.

+ [Cufflinks](http://cole-trapnell-lab.github.io/cufflinks/) - assemble and quantify transcripts. 

+ [DEXSeq](https://bioconductor.org/packages/release/bioc/html/DEXSeq.html) - identify differential exon usage.

+ [flotilla](https://github.com/yeolab/flotilla) - reproduce machine learning analysis of gene expression and alternative splicing data.

+ [GMAP and GSNAP](http://research-pub.gene.com/gmap/) - detect complex variants and splicing in short reads, SNP-tolerant.

+ [G-Mo.R-Se](http://www.genoscope.cns.fr/externe/gmorse/) - maps splice junctions to genome. 

+ [HMMSplicer](http://derisilab.ucsf.edu/index.php?software=105) - discovery canonical and non-canonical splice junctions in short read datasets.

+ [JunctionSeq](https://bioconductor.org/packages/release/bioc/html/JunctionSeq.html) - identify differential splice junctions.

+ [MapSplice](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) - map RNA-seq data to reference genome for splice junction discovery.

+ [MISO](http://genes.mit.edu/burgelab/miso/) - determine alternative splicing expression. 

+ [MMES](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798953/) - statistically determine alternative splicing.

+ [outrigger](https://github.com/YeoLab/outrigger) - calculate alternative splicing scores of RNA-Seq data based on junction reads and a de novo, custom annotation created with a graph database, especially made for single-cell analyses.

+ [rMATS](http://rnaseq-mats.sourceforge.net/) - RNA-Seq Multavariate Analysis of Transcript Splicing. [Reading rMATS output](https://www.biostars.org/p/256949/)

+ [rmats2sashimiplot](https://github.com/Xinglab/rmats2sashimiplot/) - visualize rMATS output using sashimi plots.

+ [SAW](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919401/) - identify splicing events from RNA-Seq data.

+ [Scripture](http://software.broadinstitute.org/software/scripture/) - reconstruct transcript isoforms.

+ [SingleSplice](https://github.com/jw156605/SingleSplice) - detect biological variation in alternative splicing within a population of single cells. 

+ [SpliceMap](https://web.stanford.edu/group/wonglab/SpliceMap/) - discover and align splice junctions for RNA-Seq reads.

+ [SpliceR](http://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html) - detect alternative splicing and predict coding potential. 

+ [SplicingCompass](https://www.leibniz-hki.de/en/SplicingCompass.html) - detect differential splicing using RNA-Seq data.

+ [SplitSeek](https://solidsoftwaretools.com/splitseek) - predict splice events from RNA-Seq data.

+ [STAR](https://code.google.com/archive/p/rna-star/) - identify alternative splicing.

+ [SUPPA](https://github.com/comprna/SUPPA) - identify alternative splicing.

+ [TopHat](http://ccb.jhu.edu/software/tophat/index.shtml) - map splice junctions for RNA-Seq reads.



## Databases



+ [ASIP](http://www.plantgdb.org/ASIP/) - Alternative Splicing in Plants. 

+ [ASG](https://brcwebportal.cos.ncsu.edu/asg/) - Alternative Splicing Gallery for human genes. 

+ [ASPicDB](http://srv00.recas.ba.infn.it/ASPicDB/) - Alternative Splicing PredICtion DataBase.

+ [ENSEMBL](http://useast.ensembl.org/info/genome/genebuild/genome_annotation.html) - Human and mouse genome annotations.

+ [FAST DB/Easana](https://www.easana.com/) - Friendly Alternative Splicing and Transcripts Database.

+ [Hollywood exon annotation database](http://hollywood.mit.edu/) - A website for querying a relational database of constitutive and alternative human exons, by using biological and descriptive features. 

+ [HS3D](http://www.sci.unisannio.it/docenti/rampone/) - Data set of Homo Sapiens Exon, Intron and Splice regions extracted from GenBank Rel.123. 

+ [H-DBAS](http://www.h-invitational.jp/h-dbas/) - Human-transcriptome DataBase for Alternative Splicing.

+ [MAASE](http://maase.genomics.purdue.edu/) - Convenient access, identification, and annotation of alternative splicing events (ASEs), designed specifically with experimentalists in mind.

+ [Pro-Splicer](http://prosplicer.mbc.nctu.edu.tw/) - Alternative splicing database based on protein, mRNA, and EST Sequences.

+ [SpliceNest](http://splicenest.molgen.mpg.de/) - Visualizing splicing of genes from EST Data for human, mouse, Drodophila and Arabidopsis. 



## Review of RNA-Seq splicing tools

**Tool**|**Performs split-read alignment**|**Transcript reconstruction (assembly)**|**Expression Analysis (any)**|**Gene expression analysis**|**Transcript specific expression analysis**|**Exon junction expression**|**Quantitative alternative expression analysis**|**Expression level sensitivity**|**Output**|**Minimum read length required or recommended**|**Visualization tool**|**Performs comparisons between conditions (ex. tumor vs normal)**|**Relevant comparison to Alexa-seq**|**Data type supported**|**Citation**

:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:

Alexa-Seq|N|N|Y|Y|Y|Y|Y|Junction|"Expression and structure information for junctions and genes; UCSC track info| extensive alternative expression visualization / statistics / graphs"|No minimum (tested on 36bp-100bp reads)|"Extensive| includes custom graphs and links to UCSC browser"|Y|-

Cufflinks|N|Y|Y|Y|Y|N|Y|Transcript|"Transcript information and expression statistics| BED| GTF"|75bp|UCSC browser|Y|Y

Scripture|N|Y|Y|N|N*|N|N|Transcript*|"Transcript structure information and non-parsimonious expression statistics| BED"|75bp|UCSC browser|N|N|Illumina

SpliceMap|N|N|Y|Y|N|Y|N|Junction|"Alignments. SAM| BED| Wig"|50bp|UCSC browser|N|N

TopHat|Y|N|N|N|N|Y|N|Junction|"Alignments. SAM| BED| Wig"|75bp|N|N|N

MMES|Y|N|N|N|N|Y|N|Junction|Identified splice junctions and p-values|25bp|N|N|N|Illumina|"Wang et al.

G-Mo.R-Se|Y|Y|N|N|N|N|N|Transcript*|Transcript structure information.  GFF|25bp|Grape Genome Browser|N|N|Illumina|"Denoeud et al.

SplitSeek|Y|N|N|N|N|Y|N|Junction|Alignments.  BED|50bp|UCSC browser|N|N|SOLiD only|"Ameur et al.2010

GSNAP|Y|Y|N|N|N|N|N|N/A|Alignments.  SAM and FASTA|Minimum 14bp (tested on 36bp reads)|UCSC browser|N|N|Illumina | sodium bisulfite-treated DNA sequencing (for analysis of methylation status)|"Wu and Nacu



**Tool**|**Performs split-read alignment**|**Transcript reconstruction (assembly)**|**Expression Analysis (any)**|**Gene expression analysis**|**Transcript specific expression analysis**|**Exon or Junction expression**|**Quantitative alternative expression analysis**|**Expression level sensitivity**|**Output**|**Minimum read length required or recommended**|**Ability to identify rearrangements / indels**|**Junction Identification**|**Implementation**|**Public tool**|**Open Source**

:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:

Alexa-seq|N|N|Y|Y|Y|Y|Y|Junction|"Expression and structure information for junctions and genes; UCSC track info| extensive alternative expression visualization / statistics / graphs"|No minimum (tested on 36bp-100bp reads)|N|Database|Perl/R/Unix|Y

Cufflinks|N|Y|Y|Y|Y|N|Y|Transcript|"Transcript information and expression statistics| BED| GTF"|75bp|N|Predicted from data|C++

Scripture|N|Y|Y|N|N*|N|N|Transcript*|"Transcript structure information and non-parsimonious expression statistics| BED"|75bp|N|Predicted from data|Java|Y

SpliceMap|N|N|Y|Y|N|Y|N|Junction|"Alignments. SAM| BED| Wig"|50bp|N|Predicted from data|Python

TopHat|Y|N|N|N|N|Y|N|Junction|"Alignments. SAM| BED| Wig"|75bp|N|Predicted from data|C++/Python

MMES|Y|N|N|N|N|Y|N|Junction|Identified splice junctions and p-values|25bp|N|Predicted from data|Published algorithm only|N|N/A

G-Mo.R-Se|Y|Y|N|N|N|N|N|Transcript*|Transcript structure information.  GFF|25bp|N|Predicted from data|Perl|Y**|Y

SplitSeek|Y|N|N|N|N|Y|N|Junction|Alignments.  BED|50bp|Y|Predicted from data|Perl|Y|Y (GPL)

GSNAP|Y|Y|N|N|N|N|N|N/A|Alignments.  SAM and FASTA|Minimum 14bp (tested on 36bp reads)|Y|Database or predicted form data|"Source code in C| utility programs in Perl"|Y

Tool|Performs split-read alignment|Transcript reconstruction (assembly)|Expression Analysis (any)|Gene expression analysis|Transcript specific expression analysis|Exon or Junction expression|Quantitative alternative expression analysis|Expression level sensitivity|Output|Minimum read length required or recommended|Ability to identify rearrangements / indels|Junction Identification|Implementation|Public tool|Open Source

Alexa-seq|N|N|Y|Y|Y|Y|Y|Junction|"Expression and structure information for junctions and genes; UCSC track info| extensive alternative expression visualization / statistics / graphs"|No minimum (tested on 36bp-100bp reads)|N|Database|Perl/R/Unix|Y

Cufflinks|N|Y|Y|Y|Y|N|Y|Transcript|"Transcript information and expression statistics| BED| GTF"|75bp|N|Predicted from data|C++

Scripture|N|Y|Y|N|N*|N|N|Transcript*|"Transcript structure information and non-parsimonious expression statistics| BED"|75bp|N|Predicted from data|Java|Y

SpliceMap|N|N|Y|Y|N|Y|N|Junction|"Alignments. SAM| BED| Wig"|50bp|N|Predicted from data|Python

TopHat|Y|N|N|N|N|Y|N|Junction|"Alignments. SAM| BED| Wig"|75bp|N|Predicted from data|C++/Python

MMES|Y|N|N|N|N|Y|N|Junction|Identified splice junctions and p-values|25bp|N|Predicted from data|Published algorithm only|N|N/A

G-Mo.R-Se|Y|Y|N|N|N|N|N|Transcript*|Transcript structure information.  GFF|25bp|N|Predicted from data|Perl|Y**|Y

SplitSeek|Y|N|N|N|N|Y|N|Junction|Alignments.  BED|50bp|Y|Predicted from data|Perl|Y|Y (GPL)

GSNAP|Y|Y|N|N|N|N|N|N/A|Alignments.  SAM and FASTA|Minimum 14bp (tested on 36bp reads)|Y|Database or predicted form data|"Source code in C| utility programs in Perl"|Y



\* Transcript expression values are non-parsimonious



\** Not supported (current version not stable)