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This release creates a referenceable version of the single-cell RNA-seq preprocessing pipeline.
Features include:
- Automatic download of transcriptome reference(s) for mouse and human from Gencode.
- Streamed cleaning of fastq files using htstream.
- Expression quantification using salmon or kallisto (UMI-aware).
- Automatic creation of a SingleCellExperiment container for downstream analysis in R, with statistics from preprocessing.
Upcoming
Upcoming releases will implement the following features:
- Reformatting fastq header lines using the umis tool.
- Demultiplexing of fastq files using pydemult.
- S3 / Kubernetes support for cloud-based deployments.