In this repository are the Final reports generated by DVGfinder_v3.1.py on real samples SRR8719995 - SRR8719998
The samples were published by Bosma TJ et al. (2019) and the fastQ files are available in PRJNA525871.
In each directory can find the DVGfinder output for the sample in question.
The only preprocess step consisted on interleave each pair of fastQ files in a single fastQ file per sample.
This process was done taking into account that ViReMa-a gives error when it finds readings with repeated names. For avoid that we add first "/1" or "/2" to each name read and then we made the interleaved with reformat.sh (from BBTools).
you can download the /${sample}_report.html and open in your usual browser or link in the sample of interest:
SRR8719995; SRR8719996; SRR8719997; SRR8719998
Preprint version:
- Olmo-Uceda, M.J.; Muñoz-Sánchez, J.C.; Lasso-Giraldo, W.; Arnau, V.; Díaz-Villanueva, W.; Elena, S.F. DVGfinder: A Metasearch Engine for Identifying Defective Viral Genomes in RNA-Seq Data. Preprints 2022, 2022030110 doi: 10.20944/preprints202203.0110.v1.
María José Olmo-Uceda - mariajose.olmo@csic.es
PhD student
EvolSysVir Group, I2SysBio (CSIC-UV)
Project Link: https://github.com/MJmaolu/DVGfinder
Page Link: https://mjmaolu.github.io/DVGfinder/
Under Construction
Any suggestions will be welcome 🤗