v0.9.3

Release 0.9.3

This release primarily addresses issue #59, where differences could accumulate between the value reported for a transcript in the .quant file and the sum of the associated posterior alignment probabilities in the .prob file. This was due to the display threshold filtering (i.e. removing low posterior probability alignments from the output of .prob). While each alignment may be of low probability in isolation, many of them can still affect the abundance estimate of the transcript. In 0.9.3, we change the default display threshold from 1e-3 to 1e-6, and we further expose a command line option --display-thresh, that allows the user to set a custom display threshold if they wish.

Install oarfish 0.9.3

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.9.3/oarfish-installer.sh | sh

Download oarfish 0.9.3

File	Platform	Checksum
oarfish-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
oarfish-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
oarfish-aarch64-unknown-linux-gnu.tar.xz	ARM64 Linux	checksum
oarfish-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum

v0.9.2

Install oarfish 0.9.2

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.9.2/oarfish-installer.sh | sh

Download oarfish 0.9.2

File	Platform	Checksum
oarfish-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
oarfish-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
oarfish-aarch64-unknown-linux-gnu.tar.xz	ARM64 Linux	checksum
oarfish-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum

v0.9.1

Install oarfish 0.9.1

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.9.1/oarfish-installer.sh | sh

Download oarfish 0.9.1

File	Platform	Checksum
oarfish-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
oarfish-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
oarfish-aarch64-unknown-linux-gnu.tar.xz	ARM64 Linux	checksum
oarfish-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum

v0.9.0

Install oarfish 0.9.0

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.9.0/oarfish-installer.sh | sh

Download oarfish 0.9.0

File	Platform	Checksum
oarfish-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
oarfish-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
oarfish-aarch64-unknown-linux-gnu.tar.xz	ARM64 Linux	checksum
oarfish-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum

v0.8.1

Install oarfish 0.8.1

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.8.1/oarfish-installer.sh | sh

Download oarfish 0.8.1

File	Platform	Checksum
oarfish-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
oarfish-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
oarfish-aarch64-unknown-linux-gnu.tar.xz	ARM64 Linux	checksum
oarfish-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum

v0.8.0

Install oarfish 0.8.0

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.8.0/oarfish-installer.sh | sh

Download oarfish 0.8.0

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

v0.7.3

Install oarfish 0.7.3

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.7.3/oarfish-installer.sh | sh

Download oarfish 0.7.3

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

v0.7.2

Install oarfish 0.7.2

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.7.2/oarfish-installer.sh | sh

Download oarfish 0.7.2

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

v0.7.1

Install oarfish 0.7.1

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.7.1/oarfish-installer.sh | sh

Download oarfish 0.7.1

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

v0.7.0

Install oarfish 0.7.0

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/oarfish/releases/download/v0.7.0/oarfish-installer.sh | sh

Key changes in oarfish 0.7.0

This version of oarfish brings with it several substantive changes / improvements. First, several dependencies have been upgraded to their latest major or minor versions. This includes a move to the long-awated rand 0.9. This version also adopts the latest version of minimap2-rs.

Accompanying this change is improved memory-safety and multithreaded ability. However, without any additional tuning, we noticed substantial increases in the memory requirements in raw-mapping based mode as the number of threads grows large. This has been addressed in this release, and is the result of the rather large per-thread default maximum memory allocation allowed by minimmap2. A corresponding command line option has been added to allow controlling the total thread-local buffer size, with a default of 1G (to be divided evenly over all threads). This can be controlled by the --thread-buff-size command line option.

Additionally, the coverage model has been updated and improved. We thank an anonymous reviewer for pointing out an edge case with the previous coverage model (transcripts with only 2 bins), as well as hinting at the, perhaps, unnecessary complexity of the model. In v0.7.0 we have adopted a new coverage model based on a probability obtained by passing the (mean-scaled) deviation of each bin from the expected coverage through a logistic function. The default growth rate or (k) parameter of this logistic function is set to 2, but it can be modified by the user via the --growth-rate command line option. This new coverage model has the benefit of avoiding the degenerate 2-bin case, of being conceptually simpler, and of being numerically more robust. In our testing so far, we have found that it performs similarly to, though often better than, the previous modified Binomial model. Nonetheless, since the model itself is changing, we recommend that within one analysis you ensure that all samples processed using the coverage model are processed by the same version of oarfish to avoid any potential batch effects. Samples processed without the coverage model should not exhibit any differences from the previous version.

Download oarfish 0.7.0

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