Table 1.
Transposon-insertion sequencing data analysis tools
| Name | Interface | Unique features | Transposon | URL | Ref. |
|---|---|---|---|---|---|
| INSeq pipeline | CL | Basic mapping pipeline | Any | https://www.nature.com/articles/nprot.2011.417 | 103 |
| ESSENTIALS | Web | Essentiality and conditional analysis; corrects for genomic location biases | Any | http://bamics2.cmbi.ru.nl/websoftware/essentials/essentials_start.php | 27 |
| ARTIST/conARTIST | CL | HMM-based mapping for fitness loci; sampling-based bottleneck correction | mariner | https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004782#s4 | 30 |
| TRANSIT | GUI | Bayesian, HMM and resampling-based tests | mariner | https://orca1.tamu.edu/essentiality/transit/ | 29 |
| TraDIS Toolkit | CL | Empirical essentiality analysis; comparative analysis with RNA-seq tools | Any | https://github.com/sanger-pathogens/Bio-Tradis | 31 |
| MAGenTA | CL or Web | Fitness as growth rate calculations; bottleneck correction using neutral loci; sliding window analyses | Any | https://vanopijnenlab.github.io/MAGenTA/ | 28 |
| Aerobio | CL | Fitness as growth rate calculations; bottleneck correction using neutral loci; sliding window analyses; ability to switch to RNA-seq, Term-Seq and WGS analyses | Any | https://github.com/jsa-aerial/aerobio | 32 |
| AlbaTraDIS | CL | Multicondition and gene activation analysis based on TraDIS Toolkit | Any | https://github.com/quadram-institute-bioscience/albatradis | 38 |
CL, command-line (*NIX-based) utility; GUI, stand-alone graphical user interface; HMM, hidden Markov model; RNA-seq, RNA sequencing; Term-Seq, 3′-end RNA sequencing; Web, Web-based graphical user interface; WGS, whole-genome sequencing.