Merge pull request #135 from COMBINE-lab/master

merge master back into dev

.release-please-manifest.json

@@ -1,4 +1,4 @@
 {
   "undefined": "0.5.1",
-  ".": "0.8.1"
+  ".": "0.8.2"
 }

CHANGELOG.md

@@ -2,6 +2,13 @@
 
 Changelog for alevin-fry
 
+## [0.8.2](https://github.com/COMBINE-lab/alevin-fry/compare/v0.8.1...v0.8.2) (2023-06-29)
+
+
+### Bug Fixes
+
+* update deps, make clippy happy ([ac1a316](https://github.com/COMBINE-lab/alevin-fry/commit/ac1a316001103f39a173b8a066c62810a8724875))
+
 ## [0.8.1](https://github.com/COMBINE-lab/alevin-fry/compare/v0.8.0...v0.8.1) (2023-01-12)
 
 

README.md

@@ -2,10 +2,12 @@
 
 # alevin-fry ![Rust](https://github.com/COMBINE-lab/alevin-fry/workflows/Rust/badge.svg) [![Anaconda-Server Badge](https://anaconda.org/bioconda/alevin-fry/badges/platforms.svg)](https://anaconda.org/bioconda/alevin-fry) [![Anaconda-Server Badge](https://anaconda.org/bioconda/alevin-fry/badges/license.svg)](https://anaconda.org/bioconda/alevin-fry) ![GitHub tag (latest SemVer)](https://img.shields.io/github/v/tag/combine-lab/alevin-fry?style=flat-square)
 
-`alevin-fry` is a suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data.  It consumes RAD files generated by `salmon alevin`, and performs common operations like generating permit lists, and estimating the number of distinct molecules from each gene within each cell.  The focus in `alevin-fry` is on safety, accuracy and efficiency (in terms of both time and memory usage).
+`alevin-fry` is a suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data.  It consumes RAD files generated by [`piscem`](https://github.com/COMBINE-lab/piscem) or `salmon alevin`, and performs common operations like generating permit lists, and estimating the number of distinct molecules from each gene within each cell.  The focus in `alevin-fry` is on safety, accuracy and efficiency (in terms of both time and memory usage).
 
 You can read the paper describing alevin fry, "Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data" [here](https://www.nature.com/articles/s41592-022-01408-3), and the pre-print [on bioRxiv](https://www.biorxiv.org/content/10.1101/2021.06.29.450377v1).
 
+**Note**: We recommend using [`piscem`](https://github.com/COMBINE-lab/piscem) as the back-end mapper, rather than salmon, as it is substantially more resource-frugal, faster, and is a larger focus of current and future development.
+
 ### Getting started with `alevin-fry` and dedicated documentation
 
 While this `README` contains some useful information to get started and some pointers, `alevin-fry` has it's own [dedicated documentation site](https://alevin-fry.readthedocs.io/en/latest/), hosted on `ReadTheDocs`.