Check mulitple software options for tRNA module - Githubissues

HCGB-IGTP / XICRA

Small RNAseq pipeline for paired-end reads

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Check mulitple software options for tRNA module #11

Open JFsanchezherrero opened 2 years ago

JFsanchezherrero commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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/