Welcome to the documentation for piscem-infers!#
What is piscem-infer?#
piscem-infer is a tool to perform quantification of some target (e.g. transcripts in RNA-seq, strains or species in metagenomic sequencing) using statistical inference to arrive at an abundance estimate for each target and, optionally, an associated uncertainty for each estimate.
The piscem-infer tool consumes bulk-RAD files (produced by piscem or piscem-cpp) and to produce from them abundance estimates of the targets against which the reads were mapped. For example, a basic RNA-seq pipeline could consist of mapping the reads against the transcriptome using piscem, and then quantifying transcript abundance using piscem-infer. Likewise, one could use the pair of tools on metagenomic index and metagenomic sequencing reads to perform taxonomic abundance estimation. The main goal of piscem-infer is to separate the statistical inference algorithms and code from the code that performs indexing and mapping. This allows faster and more agile development of new improvements to the inference method, as well as eases the maintenance burden.
The piscem-infer program is written in rust, which makes it easy for end-users to compile, and which also makes it easy for us to deploy without the need for end-users to compile it (it’s easy to create statically-linked, pre-compiled executables, and to put the package on bioconda). At the same time, this provides access to the safety guarantees of rust, making the code easier to develop, maintain, and run, with confidence, while retaining the efficiency of a high-performance, statically-typed, compiled language.
While piscem-infer is in active development, it is already very usable! We encourage folks who are curious to try it out, to open GitHub issues for any questions or feature requests, and to provide feedback on how you’d like to see this next “evolution” of (bulk sequencing) abundance estimation tools evolve!
Check out the Usage section for further information.
Note
This project is under active development.