Analysis of single-cell RNA-seq data begins with pre-processing of sequencing reads to generate count matrices. We investigate algorithm choices for the challenges of pre-processing, and describe a workflow that balances efficiency and accuracy. Our workflow is based on the kallisto (<https://pachterlab.github.io/kallisto/>) and bustools (<https://bustools.github.io/>) programs, and is near-optimal in speed and memory. The workflow is modular, and we demonstrate its flexibility by showing how it can be used for RNA velocity analyses. Documentation and tutorials for using the kallisto | bus workflow are available at <https://www.kallistobus.tools/>.
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- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
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