finder is a gene annotator pipeline that automates the process of downloading short reads, aligning them, and using the assembled transcripts to generate gene annotations. Additionally, it uses protein sequences and reports gene predictions by BRAKER2. It is a fast, scalable, platform-independent software that generates gene annotations in GTF format. finder accepts inputs through the command-line interface. It finds several novel genes/transcripts and also reports the tissue/conditions they were found to be in. finder is released as a docker image. Users need to have python3 installed in their system to be able to run finder. The header script will create either a docker container or a singularity container depending on what is installed on the system with preference given to docker.

If you use finder for your research please cite

Sagnik Banerjee, Priyanka Bhandary, Margaret Woodhouse, Taner Z Sen, Roger P Wise, and Carson M Andorf. FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences BMC Bioinformatics

Major changes

1. Conda environment replaced with docker image. The header program will execute finder either in a docker or in a singularity environemnt.
2. GeneMark S/T has been replaced with CodAn for predicting coding regions of genes.
3. GeneMark E/T is still required by finder to generate gene predictions. We will explore the option of replacing this in a future release to make finder entirely automated.

Refer to https://github.com/sagnikbanerjee15/Finder/blob/master/Changelog.md to view all the changes in detail.

Please report all issues to https://github.com/sagnikbanerjee15/Finder/issues.

finder is a gene annotator pipeline that automates the process of downloading short reads, aligning them, and using the assembled transcripts to generate gene annotations. Additionally, it uses protein sequences and reports gene predictions by BRAKER2. It is a fast, scalable, platform-independent software that generates gene annotations in GTF format. finder accepts inputs through command-line interface. It finds several novel genes/transcripts and also reports the tissue/conditions they were found to be in. For this version, no docker images could be provided due to distribution restrictions of the underlying software.

If you use finder for your research please cite

Sagnik Banerjee, Priyanka Bhandary, Margaret Woodhouse, Taner Z Sen, Roger P Wise, and Carson M Andorf. FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences BMC Bioinformatics

What's Changed

• default to not keeping the STAR index in shared memory by @eernst in https://github.com/sagnikbanerjee15/Finder/pull/22

New Contributors

• @eernst made their first contribution in https://github.com/sagnikbanerjee15/Finder/pull/22

Full Changelog: https://github.com/sagnikbanerjee15/Finder/blob/finder_v1.0.0/Changelog.md