Check mulitple software options for tRNA module

[JFsanchezherrero]

Multiple options to create tRNA analysis from small RNAseq data:

MINTmap:

• Code/software: https://github.com/TJU-CMC-Org/MINTmap/tree/release/v2.0-alpha
• Paper: https://www.nature.com/articles/srep41184
• Web: https://cm.jefferson.edu/mintmap/

tRNAExplorer:

• Code/software: https://github.com/hqyone/tRNAExplorer
• Paper: https://www.nature.com/articles/s41598-021-83469-6

tDRmapper:

• Code/software: https://github.com/sararselitsky/tDRmapper
• Paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0800-0
• Web: https://blogs.cornell.edu/sethupathylab/bioinfotools/

mirge3:

• Documentation: https://mirge3.readthedocs.io/en/latest/
• Code: https://github.com/mhalushka/mirge3.0/
• Paper: https://academic.oup.com/nargab/article/3/3/lqab068/6325159

mim-tRNAseq:

• Code/software: https://github.com/nedialkova-lab/mim-tRNAseq
• Paper: https://doi.org/10.1016/j.molcel.2021.01.028
• Web: https://www.biochem.mpg.de/nedialkova

tRAX: GtRNAdb mapper:

• Code: https://github.com/UCSC-LoweLab/tRAX
• Docs: http://trna.ucsc.edu/tRAX/#tutorial
• Paper: http://trna.ucsc.edu/tRAX/citation/ (submitted)

[JFsanchezherrero]

There is an additional package: iso-tRNA-CP have not been able to find link yet to softare. Here link to paper: https://www.pnas.org/cgi/doi/10.1073/pnas.1821120116

[JFsanchezherrero]

Also, there is a database GtRNAdb (http://gtrnadb.ucsc.edu/) and associate software:

• tRNAscan-SE web server and source code
• tRNAviz - explore and visualize tRNA sequence features
• tDRnamer - standardized naming for tRNA-derived RNAs
• tRAX - tRNA and tRNA-derived RNA sequencing data analysis package
• tRAP - tRNA gene Activity Predictor

Naming tRNAs:
http://gtrnadb.ucsc.edu/docs/naming/