evolinc / evolinc-ii

EVOLINC-II 2.0

Evolinc-II pipeline is designed to perform a series of comparative genomic and transcriptomic analyses across an evolutionary timescale of the user’s choosing and on any number (1-1000s) of query lincRNAs. Please see our chapter in Plant Comparative Genomics for a detailed explanation on how to use Evolinc-II in your research (https://link.springer.com/protocol/10.1007/978-1-0716-2429-6_3).

Evolinc-II minimally requires the following input data:

1. A FASTA file of lincRNA sequences of all genomes to be interrogated.
2. A single column text file with all species listed in order of phylogenetic relatedness to the query species. See Discussion_on_species_list.txt for more info.
3. Evolinc-II can optionally incorporate genome annotation files (GTF) and known lincRNA datasets from target species in FASTA format.
4. Currently, Evolinc-II iterates through all of its analyses using a tab-delimited file that contains all of this information, including file names and species abbreviations. See Discussion_on_BLASTing_file.md for more info.

Availability

Using a Docker image

Since there are several dependencies (can be seen in Dockerfile) for running Evolinc-II on your linux or MAC OS, we highly recommend using the Docker image for Evolinc-II or use the Dockerfile to build an image and then use the built image.

# Pull the image from CyVerse Dockerhub
docker pull evolinc/evolinc-ii:2.0

# See the command line help for the image
docker run evolinc/evolinc-ii:2.0 -h

# Download the test data
wget https://github.com/Evolinc/Evolinc-II/releases/download/v1.0/sample_data.zip
unzip sample_data.zip

# Run Evolinc-II on the test data
docker run --rm -v $(pwd):/working-dir -w /working-dir evolinc/evolinc-ii:2.0 -b sample_data/Blasting_list.txt -l sample_data/Sample_query_lincRNA_data_set_for_webinar.fasta -q Atha -i sample_data -s sample_data/test_species_list.txt -o test_out -v 1e-20 -n 8

Using CyVerse Discovery Environment

The Evolinc-II app is currently integrated in CyVerse’s Discovery Environment and is free to use by researchers. The complete tutorial is available at this CyVerse wiki. If you do not have access to a high performance computing cluster we highly recommend using Evolinc-II within the DE. Limited computing resources can lead to extremely long Evolinc-II run times, especially when searching through large genomes. Not only is the CyVerse DE free to researchers, but many of the genomes are already integrated (and almost all others are available through CoGe; genomevolution.org), thereby alleviating the data storage hurdle common with these types of analyses.

Issues

If you experience any issues with running Evolinc-I (DE app or source code or Docker image), please open an issue on this github repo.

Copyright free

The sources in this github repository are copyright free. Thus you are allowed to use these sources in which ever way you like. Please be aware that other license terms apply for the Notung.jar used inside the image. Here is the full MIT license.

Citing Evolinc-II

If you have used Evolinc in your research, please cite the below manuscripts.

Andrew D. Nelson*, Upendra K. Devisetty*, Kyle Palos, Asher K. Haug-Baltzell, Eric Lyons, Mark A. Beilstein (2017). "Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifying sequence conserved lincRNAs for functional analysis". Frontiers in Genetics. 1(10)

Anna C. Nelson Dittrich and Andrew D. L. Nelson (2022). "High-Throughput Evolutionary Comparative Analysis of Long Intergenic Noncoding RNAs in Multiple Organisms". Plant Comparative Genomics (Part of the Methods in Molecular Biology Book Series)

evolinc-ii's Issues

Create "intronic space" parameter

Allow for variable distance for removing gaps and merging hits on similar scaffolds (max gap length currently set to length of query lncRNA).

Replace BLAST with LAST to improve performance.

Replace underscores in FASTA headers with "."

Bed file is perceived as a quant file by CoGe

Need to modify the code to make the bed file a gff instead (perhaps a CoGe-specific issue).

please add the option for multiple processes when running the blastn

I notice that the EvoLinc-2 only use 4 thread. But Our server cluster have more than 128 thread per node. And, my task, even one ninght passed, didn't done just one species. We have 18 species together. I cann't image how long it will take. Please tell me how to set the multiple threading or multiple processes. Thank you a lot!

Scan through sequence homologs for coding potential

It would be nice to screen through all identified sequence homologs (the ones that don't have any annotation) with Evolinc-I to see if they are also putative lncRNAs.