TABLE 1.
List of the Iso-Seq tools along with a brief description of their usage and related online links.
| Tool | Usage | Website | Literature |
|---|---|---|---|
| ASTALAVISTA | Detect alternative splicing events | http://astalavista.sammeth.net/ | Foissac and Sammeth,2007 |
| CASH | Detect alternative splicing events | https://sourceforge.net/projects/cash-program/ | Wu et al.,2018 |
| CodingQuarry | Gene prediction (HMM-based) using both RNA-Seq data and genome sequence | https://sourceforge.net/projects/codingquarry/ | Testa et al.,2015 |
| GMAP | Spliced alignment to genome | http://research-pub.gene.com/gmap/ | Wu and Watanabe,2005 |
| LoRDEC | Error correction of FLNC with short read RNA-seq | http://atgc.lirmm.fr/lordec | Salmela and Rivals,2014 |
| LoReAn | Comparative analysis and annotation: identify novel isoforms/genes against reference annotation | https://github.com/lfaino/LoReAn | Cook et al.,2018 |
| LSC | Error correction of FLNC with short read RNA-seq | http://augroup.org/LSC/LSC_download.html | Au et al.,2012 |
| minimap2 | Spliced alignment to genome | https://github.com/lh3/minimap2 | Li,2018 |
| PASA | Detect alternative splicing events | https://pasapipeline.github.io/ | Liu et al.,2017 |
| Proovread | Error correction of FLNC with short read RNA-seq | https://github.com/BioInf-Wuerzburg/proovread | Hackl et al.,2014 |
| Quiver | Polishing PacBio RS II reads | https://github.com/PacificBiosciences/ GenomicConsensus | Chin et al.,2013 |
| SpliceGrapher | Detect alternative splicing events | http://splicegrapher.sourceforge.net/ | Rogers et al.,2012 |
| SQANTI | Comparative analysis and annotation: identify novel isoforms/genes against reference annotation | https://bitbucket.org/ConesaLab/sqanti | Tardaguila et al.,2018 |
| STAR | Spliced alignment to genome | https://github.com/alexdobin/STAR/releases | Dobin et al.,2013 |
| SUPPA | Detect alternative Splicing events | https://bitbucket.org/regulatorygenomicsupf/suppa | Alamancos et al.,2015 |
| TAPIS | Alternative splicing, collapsing redundant or degraded transcripts | https://bitbucket.org/comp_bio/tapis | Abdel-Ghany et al.,2016 |
| ToFU | Preprocessing (collapse to non-redundant isoforms) | https://github.com/PacificBiosciences/IsoSeq_SA3nUP | Gordon et al.,2015 |