Not your papa's FASTQ files.
ReadDatastores provides a set of datastore types for storing and randomly accessing sequences from read datasets from disk. Each datastore type is optimised to the type of read data stored.
Using these data-stores grants greater performance than using text files that store reads (see FASTX.jl, XAM.jl, etc.) since the sequences are stored in BioSequences.jl succinct bit encodings already, and preset formats/layouts of the binary files means no need to constantly validate the input.
- A paired read datastore is provided for paired-end reads and long mate-pairs (Illumina MiSeq etc).
- A long read datastore is provided for long-reads (Nanopore, PacBio etc.)
- A linked read datastore is provided for shorter reads that are linked or grouped using some additional (typically proximity based) tag (10x).
Also included is the ability to buffer these datastores, sacrificing some RAM, for faster iteration / sequential access of the reads in the datastore.
You can install ReadDatastores from the julia
REPL. Press ] to enter pkg mode again, and enter the following:
add ReadDatastoresIf you are interested in the cutting edge of the development, please check out the master branch to try new features before release.
ReadDatastores is tested against Julia 1.X on Linux, OS X, and Windows.
Latest build status:
We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.
Take a look at the contributing files detailed contributor and maintainer guidelines, and code of conduct.
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