taf-trinity

taf-trinity packages Trinity 2.15.2-r2 for de novo RNA-seq transcriptome assembly.

Package identity:

• name: trinity
• command: taf-trinity
• kind: tool
• TAFFISH version: 2.15.2-r2
• container image: ghcr.io/taffish/trinity:2.15.2-r2
• upstream release: Trinity-v2.15.2
• runtime version string: Trinity version: Trinity-v2.15.2
• source archive: trinityrnaseq-v2.15.2.FULL.tar.gz
• source SHA256: baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c

What Is Included

This app builds Trinity from the official FULL release archive and includes the core Trinity assembly stack:

• Trinity
• Inchworm and Chrysalis binaries
• Butterfly Java jar from the upstream release archive
• Trinity utility scripts such as TrinityStats.pl, insilico_read_normalization.pl, align_and_estimate_abundance.pl, and abundance_estimates_to_matrix.pl
• built bundled helpers: ParaFly, seqtk-trinity, bamsifter, slclust, and collectl
• runtime tools required by the main Trinity path: Java, Perl, Python 3 with NumPy, Jellyfish 2, Bowtie2, Salmon, Samtools, and BLAST+

The default TAFFISH command runs the upstream Trinity script directly:

taf-trinity -- --seqType fq --max_memory 20G \
  --left reads_1.fq.gz \
  --right reads_2.fq.gz \
  --CPU 8 \
  --output trinity_out_dir

The output directory name must contain trinity, following Trinity's own safety check.

Command Mode

taf-trinity --help prints this app's wrapper help. Use -- to pass option-leading arguments to the default upstream command:

taf-trinity -- --help
taf-trinity -- --version
taf-trinity -- --seqType fq --single reads.fq.gz --max_memory 10G --CPU 4 --output trinity_single_out

Because this is a normal tool app with command mode enabled, helper commands can be run in the same container:

taf-trinity Trinity --version
taf-trinity TrinityStats.pl trinity_out_dir.Trinity.fasta
taf-trinity insilico_read_normalization.pl --help
taf-trinity salmon --version
taf-trinity bowtie2 --version

For upstream utilities, prefer command mode with the real utility name rather than trying to treat utility names as Trinity subcommands.

Common Workflows

Paired-end de novo assembly:

taf-trinity -- --seqType fq --max_memory 50G \
  --left left.fq.gz \
  --right right.fq.gz \
  --CPU 16 \
  --output trinity_paired_out

Single-end de novo assembly:

taf-trinity -- --seqType fq --max_memory 20G \
  --single reads.fq.gz \
  --CPU 8 \
  --output trinity_single_out

Run Trinity statistics:

taf-trinity TrinityStats.pl trinity_paired_out.Trinity.fasta

In-silico read normalization:

taf-trinity insilico_read_normalization.pl --seqType fq --JM 20G \
  --left left.fq.gz \
  --right right.fq.gz \
  --pairs_together \
  --CPU 8 \
  --output trinity_norm

Boundaries

This package is intended to cover Trinity's main de novo assembly path and the core helpers needed by that path. It does not attempt to reproduce the full upstream Docker image's large downstream analysis environment. In particular, R/Bioconductor packages, RSEM, kallisto, eXpress, STAR, HISAT2, GMAP, BLAT, Picard/GATK, FastQC, MultiQC, and differential-expression plotting/reporting stacks are not bundled here unless they are already listed above.

align_and_estimate_abundance.pl can use Salmon in this image. Modes that require RSEM, kallisto, eXpress, or extra aligners should be run with separate TAFFISH apps or a dedicated downstream workflow.

Genome-guided and long-read-assisted modes are partially covered by Samtools and BLAST+ in this image, but paths that require external alignments, Picard, GATK, site-specific grid schedulers, or large reference resources remain user-supplied workflow concerns.

Trinity's --version command performs an upstream network check when curl is available. This runtime image intentionally does not install curl; the command still prints Trinity version: Trinity-v2.15.2 and then reports that it could not run the network check.

Platform

The image is built from source on Ubuntu 24.04 and is intended for native linux/amd64 and linux/arm64 container platforms. Trinity jobs can be memory and CPU intensive; set --max_memory and --CPU explicitly for reproducible runs.

License Boundary

The TAFFISH app packaging files are licensed under Apache-2.0. The packaged upstream Trinity software is covered by: BSD-3-Clause with bundled third-party components including ParaFly, seqtk-trinity, Trimmomatic, collectl, bamsifter/htslib, and Ubuntu-packaged runtime tools. Bundled third-party components, datasets, models, and external resources keep their own license terms.

Upstream

• Upstream repository: https://github.com/trinityrnaseq/trinityrnaseq
• Upstream release: https://github.com/trinityrnaseq/trinityrnaseq/releases/tag/Trinity-v2.15.2
• Running Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-Trinity
• Upstream license: BSD-3-Clause for Trinity itself, with additional bundled and Ubuntu-packaged third-party components under their respective licenses.

Primary citations:

• Grabherr et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. DOI: 10.1038/nbt.1883, PMID: 21572440.
• Haas et al. 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. DOI: 10.1038/nprot.2013.084, PMID: 23845962.