v0.6.3

Install oarfish 0.6.3

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.6.3/oarfish-installer.sh | sh

Download oarfish 0.6.3

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

v0.6.2

Changes

This version fixes a potential bug in raw-read based mode (which was introduced in v0.6.1) when using the coverage model. A shift of 1 base (due to a 0-1 coordinate transform) could cause a mapped position to extend past the end of a transcript and prevent running with the coverage model enabled on some data. This version addresses that bug.

This also bumps the versions of some dependencies.

Install oarfish 0.6.2

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.6.2/oarfish-installer.sh | sh

Download oarfish 0.6.2

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

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

v0.5.1

New features

oarfish now outputs a file of the form <output_stem>.ambig_info.tsv. This file has a number of rows equal to the number of transcripts in the quantified transcriptome (plus a header). It records, for each transcript (in the same order in which they appear in <output_stem>.quant) the number of unique, ambiguous, and total (unique + ambiguous) reads aligning to each transcript.

Improvements

oarfish v0.5.1 will dedicate > 1 thread to bam file chunk decompression if >2 threads are passed on the command line.

Install oarfish 0.5.1

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.5.1/oarfish-installer.sh | sh

Download oarfish 0.5.1

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

v0.5.0

Install oarfish 0.5.0

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.5.0/oarfish-installer.sh | sh

Download oarfish 0.5.0

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

v0.4.0

Install oarfish 0.4.0

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.4.0/oarfish-installer.sh | sh

Download oarfish 0.4.0

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

v0.3.1

Install oarfish 0.3.1

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.3.1/oarfish-installer.sh | sh

Download oarfish 0.3.1

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

v0.3.0

oarfish 0.3.0

This version contains a major new feature and a small bug fix from 0.2.0.

• This version addresses a collision in the short command line option -t in version 0.2.0, which was used both for the number of threads and the 3' clip distance. In version 0.3.0, the short option for threads is -j instead. The long options for both arguments remains the same.

• This version adds support for the generation of inferential replicates via bootstrap sampling. oarfish now accepts a parameter --num-bootstraps (default value of 0). If you pass a value > 0, then, after the main inference, oarfish will draw the requested number of bootstrap replicates. The samples (expected counts) are written to a parquet data frame in a file specified by <outputstem>.infreps.pq.

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.3.0/oarfish-installer.sh | sh

Download oarfish 0.3.0

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

v0.2.0

Install oarfish 0.2.0

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.2.0/oarfish-installer.sh | sh

Download oarfish 0.2.0

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