v0.6.1

Install oarfish 0.6.1

Release 0.6.1 adds two substantial new features to oarfish. Both are currently considered to be in beta, but have been tested and appear to work well. However, as always, please report on GitHub if you run into any unexpected issues.

New Features

read-based mode

The first new feature is the capability to quantify directly from a reference and sequencing reads (i.e. bypassing the need to first generate a bam file). To perform this task, oarfish takes advantage of the excellent minimap2-rs library. When run in this mode, oarfish will index the reference transcriptome and then align the reads against this index (you can also pass a pre-built index in place of the reference if you have one). This allows one to align and quantify transcript abundance in a single-command, avoids the need to generate a potentially large intermediate bam file, and also minimizes the possibility of using wrong or sub-optimal mapping parameters. When using this mode, you must also provide the --seq-tech argument; see the documentation for more details.

single-cell quantification

This release incorporates the first single-cell quantification capabilities. Given a bam file, collated by cell barcode and with already (UMI) deduplicated reads, this mode, enabled with the --single-cell flag, will allow oarfish to produce a single-cell quantification matrix. Currently, this mode cannot be used with read-based mode, and the input bam file should be properly formatted for this purpose (i.e. all alignment records for the same cell barcode should be adjacent in the bam file, and a count will be obtained for each read record, so UMI de-duplication should have been performed if those are the counts you want). In the future, counting UMIs directly may be supported, and some of these other restrictions may be lifted.

Improvements

It is now easier (trivial) to override parameters present in a filter-group. That is, if you choose an existing filter-group, and then additionally provide specific values for any of the filters, the provided individual values will override the default values of the filter group. This behavior mimics the "preset"/override behavior of other tools like minimap2 and should increase the usability of the filter groups. It is particularly helpful for overriding directional filters (i.e. to keep only alignments in a certain orientation).

Other various enhancements, including a nice spinner to show progress when processing a bam file or raw reads, has been added.

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.6.1/oarfish-installer.sh | sh

Download oarfish 0.6.1

File	Platform	Checksum
oarfish-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
oarfish-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
oarfish-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum