We introduce alevin, an efficient pipeline for gene quantification from dscRNA-seq (droplet-based single-cell RNA-seq) data. Alevin is an end-to-end quantification pipeline that starts from sample-demultiplexed FASTQ files and generates gene-level counts for two popular droplet-based sequencing protocols (drop-seq , and 10x-chromium ). Importantly, alevin handles all processing internally, avoiding reliance on external pipeline programs, and the need to write large intermediate files to disk. Alevin adopts efficient algorithms for cellular-barcode whitelist generation, cellular-barcode correction, lightweight per-cell UMI deduplication and quantification. This integrated solution allows alevin to process data much faster (typically ~ 10 times faster) than other approaches, while also working within a reasonable memory budget. This enables full, end-to-end analysis for single-cell human experiment consisting of ~ 4500 cells with 335 Million reads with 13G of RAM and 8 threads (of an Intel Xeon E5-2699 v4 CPU) in 27 minutes.
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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.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!