• updated docker (and apptainer/singularity) to ubuntu 24.04
• bamsifter compilation issue addressed
• minor updates to accessory scripts

Trinity-v2.15.1 Feb 5, 2023

• bamsifter update to ease compilation issues
• update to contig_ExN50_statistic.pl to provide either transcript (default) or gene based analysis (note, both use the isoform expression matrix!)
• inclusion of try_estimate_TPM_filtering_threshold.Rscript, which tries to estimate the count of transcripts with sufficient expression.

** download the FULL version ** as it contains the required submodules

Trinity-v2.15.0 Nov 30, 2022

• use DB_File for storing read names wanted during normalization step eliminating excessive RAM usage.
• support for hpc_gridrunner/singularity
• Docker updated to ubuntu:20.04

** download the FULL version ** as it contains the required submodules

Trinity-v2.14.0 Mar 11, 2022

• bugfix for the rarely occurring butterfly error: "after topo sort, still have edge unaccounted for: Edge..."
• setting max value for max_mem to 200G to avoid potential problems
• adding validate_fastqs.py
• setting an imposed absolute min contig length parameter setting to 100
• exit zero on version check
• updates from M. Crusoe to make system
• updated bowtie2 and samtools sort command
• added trinity ids for the goseq depleted files

Trinity-v2.13.2 Sep 4, 2021

-bugfix - Trinity-GG final output files werent being written in v2.13, so restored here under v2.13.2, and integrated into the test regression suite to check in future releases.
-max reads per graph setting utilized when writing partitioned fa files from phase1 into phase2, prioritizing highest pct read mapping to graph and read pairings - handles the problem of a small number of graphs becoming sinks for reads with minimal spectral kmer alignments

Trinity-v2.13.1 Aug 23, 2021

-bugfix in Trinity gene splice modeler causing rare crashes

** download the FULL version ** which contains the required submodules

Trinity-v2.13.0 Aug 11, 2021

-moved salmon filtering to the end of genome-free assembly, while retaining per-cluster execution with genome-guided.
-parafly progress monitoring resumes instead of resets under retry mode.
-added --no_symlinks option for those that can't use symlinks
-min contig length better enforced
-improved Butterfly stability

** download the FULL version ** as it contains the required submodules

Trinity-v2.12.0 Mar 4, 2021

-major:
-Butterfly code updates to improve speed for other long-running challenging assemblies.
-minor:
-in silico normalization - random seed set for reproducibile read selection.
-misc updates to improve upon reproducible execution - still some work to do here on various components.
-using current STAR aligner in docker: 2.7.8a
-begin of support for long reads in genome-guided pipeline
-providing WDL pipelines as used on Terra, DNAnexus, etc.

download the *FULL.tar.gz version.

Trinity-v2.11.0

-major:
-bamsfiter upgrade & bugfix for genome-guided assembly
-improved performance on complex data sets:
-chrysalis pct kmers read to cluster assignment in phase 1 to 10% and phase 2 to 50%
-inchworm set to use min kmer entropy 1.0 during phase 1
-iworm contig clustering set to min len 100 during phase 1
-minor:
-added option --no_parallel_norm_stats to reduce ram requirements for normalization
-ptr update, hc_samples and order by sample compatibility update

Trinity-v2.10.0 Mar 18, 2020

-added bamsifter for genome-guided Trinity-based aligned read normalization pre-assembly
-DTU updates for py3
-docker/singularity updates: now uses R-3.6.3 and py3
-improved error handling and test coverage in trinity-seqtk
-can specify read groups in variant detection pipeline runner
-kmer size can be adjusted again for experimental purposes only
-R less verbose on exec
-minor bugfixes