ORP Release 2.3.3

change inflation to 12

ORP Release 2.3.2

ORP Version 2.3.2 <- 2.3.1

• update docker base image to Ubuntu 20.04 and new docker image
• update software version for Orthofinder 2,5,2, BUSCO 5.1.2, Trinity 2.12, SPAdes 3.15.2, diamond 2.0.8, RCORRECTOR 1.04
• handle a corner case there TPM filter does not remove any transcripts, which in previous versions caused a crash.
• change to use mamba during install

ORP Release 2.2.8

Fix a minor but in reporting the number of unique transcripts, which was identified by Adnan Moussalli.

ORP Release 2.2.7

CHANGELOG:

• Bugs fixed that lead to a smoother execution.
• add "Percent properly paired" metric to report.
• Added nextera adapters to list of things to be trimmed.
• docker pull macmaneslab/orp:2.2.7

ORP release 2.2.3

Change log

1. Changes are related to the Dockerfile, to make the install process easier.
2. The software can not be installed via docker pull macmaneslab/orp:ebi2019
3. A new optional flag, BUSCO_THREADS, which allows you to set the number of BUSCO threads independently from threads used in the rest of the pipeline, which might be needed as there is potentially some new weirdness with BUSCO/BLAST.

ORP release 2.2.2

Changelog Version 2.2.0

• FIXED a critical bug whereby the incorrect transcript was picked from a given orthogroup. This fix will potentially improve BUSCO scores dramatically.
• The ORP can now be installed via Docker!! See Dockerfile/Dockerfile
• ADDED a flag to filter lowly expressed transcripts out of the dataset. Implement via TPM_FILT=<float>. The unfiltered assembly is available in the assemblies/working/ folder. We also implement some methods to try and make sure that we don't eliminate any "real" transcripts in this process of TPM filtering.
• ADDED a check to make sure that your read files exist at the specified location.
• FIXED a bug the prevented proper BUSCO checkpointing (thanks @AdamStuckert).
• UPDATED Salmon to 0.13.1 and added the --validateMappings flag to the Salmon commands.
• UPDATED code such that you no longer need to specify main when running oyster.mk.

ORP release 2.1.2

Changelog:

• This release contains no new assembly functionality.
• Changes have been made to greatly improve the speed of the installation, specifically the "solving environment" stage in conda. See bioconda/bioconda-recipes#13774 for some info.

ORP version 2.1.1

Change log for Version 2.1.1

• Updated conda environment name to orp rather than orp_v2
• Users may now specify kmer length to be used for Trinity using flag TRINITY_KMER=INT and for SPAdes using flags SPADES1_KMER=INT for the 1st SPAdes run and SPADES2_KMER=INT for the 2nd SPAdes run. Note the max kmer for trinity is 32, and for SPAdes it is 96. For all assemblies, the kmer length must be read_length-1 at a maximum.
• Add a check to make sure reads are of sufficient length given your selected assembly kmer length

2.1.0

Changelog for Version 2.1.0

• Strand specific libraries are now assembled properly, this is enabled by adding the STRAND= flag. Both RF and FR are options, tho RF is the most common option.
• There is a new tool, strandeval.mk, which helps you evaluate the strandedness of your assembly. This evaluation is now run a the end of the main assembly tool, as well as part of the report generation tool.
• There is a new tool, report.mk, which generates an assembly report for you.
• There is a new tool, quant.mk, which facilities the quantitation procedure.
• Typing oyster.mk help, report.mk help, strandeval.mk help will print a help message.

As usual, see https://oyster-river-protocol.readthedocs.io/en/latest/ for installation and other details.

2.0.0

This is a major new release and everybody is encouraged to update. Because this release contains tons of new functionality, it's entirely possible that a simple git pull from your existing repo will fail (sorry about that). Better to install in a new location, and potentially delete the old. The install from fresh, see http://oyster-river-protocol.readthedocs.io/en/latest/aws_setup.html

Change log

• The use of LinuxBrew has been removed, in favor of conda. Dependencies are now managed by conda. You will need to launch the orp_v2 conda environment, which is created by make, before assembling.
• The final assembly is now called $RUNOUT.ORP.fasta.
• Shannon has been removed, and TransABySS has been added in it's place. MANY users (and myself) have struggled with the RAM use and runtime of Shannon. TransABySS is much faster, and uses much less RAM.
• Diamond is leveraged for transcript recovery. It had been noted by some users that a few "real" transcripts were getting lost during the OrthoFuser steps.. Diamond, which is run after, recovers those.
• cd-hit-est is now run at the end of the assembly process, using a 98% threshold. This removes many identical (or nearly so) transcripts from the assembly.
• The report that is printed at the end of the assembly has been enhanced.