Open source

Verdanta.tech is a curated plant RNASeq database. Please visit our front page if you are interested in the project’s nature.

Our main software stack, featuring the front end, back end, and processing pipeline, is written in Rust and is not open source. There are, however, two open-source components we are sharing under the permissive MIT license.

• Serde-saphyr is a strongly typed YAML reader and writer, critical for Verdanta due to its extended writing capabilities. YAML is the primary format we use to ship metadata. Serde-saphyr supports creating anchors from references, putting short comments where needed, and formatting larger sections of text nicely. We did not find a Rust library that met these requirements, so we wrote our own.

• Thaf is a command-line tool to extract transcript sequences from a genome FASTA file based on GFF3 annotation files. It can also generate transcript-to-gene mapping files compatible with tools such as Salmon. We needed to quickly develop this tool because the widely known alternative we would otherwise have used was crashing with a segmentation fault on one of our genomes. Being a Rust application, that is much less prone to fail due to unexpected reasons while providing performance comparable to C++. Verdanta aims to support arbitrary transcriptomes; hence, transcript extraction from the pipeline is expected to be robust and fast.