---
name: "Trinity"
section: "1"
platform: "linux"
package: "trinityrnaseq"
version: "2.15.2+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Trinity"
---

# Trinity(1)

RNA-Seq De novo Assembly

## NAME

Trinity - RNA-Seq De novo Assembly

## DESCRIPTION

Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.

## OPTIONS

Required:

-

  **--seqType** \<string\> type of reads: ( fa, or fq )

-

  **--max\_memory** \<string\> suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc) provied in Gb of RAM, ie.  '--max\_memory 10G'

If paired reads:

-

  **--left**  \<string\> left reads, one or more (separated by space)

-

  **--right** \<string\> right reads, one or more (separated by space)

Or, if unpaired reads:

-

  **--single** \<string\> single reads, one or more (note, if single file contains pairs, can use flag: **--run\_as\_paired** )

Misc:

-

  **--SS\_lib\_type** \<string\> Strand-specific RNA-Seq read orientation. if paired: RF or FR, if single: F or R.   (dUTP method = RF) See web documentation.

-

  **--CPU** \<int\> number of CPUs to use, default: 2

-

  **--min\_contig\_length** \<int\> minimum assembled contig length to report (def=200)

-

  **--long\_reads** \<string\> fasta file containing error-corrected or circular consensus (CCS) pac bio reads

-

  **--genome\_guided\_bam** \<string\> genome guided mode, provide path to coordinate-sorted bam file. (see genome-guided param section under **--show\_full\_usage\_info**)

-

  **--jaccard\_clip** option, set if you have paired reads and you expect high gene density with UTR overlap (use FASTQ input file format for reads). (note: jaccard\_clip is an expensive operation, so avoid using it unless necessary due to finding excessive fusion transcripts w/o it.)

-

  **--trimmomatic** run Trimmomatic to quality trim reads see '--quality\_trimming\_params' under full usage info for tailored settings.

-

  **--normalize\_reads** run in silico normalization of reads. Defaults to max. read coverage of 50. see '--normalize\_max\_read\_cov' under full usage info for tailored settings.

-

  **--no\_distributed\_trinity\_exec** do not run Trinity phase 2 (assembly of partitioned reads), and stop after generating command list.

-

  **--output** \<string\> name of directory for output (will be created if it doesn't already exist) default(your current working directory)

-

  **--full\_cleanup** only retain the Trinity fasta file, rename as ${output\_dir}.Trinity.fasta

-

  **--cite** show the Trinity literature citation

-

  **--version** reports Trinity version (Trinity\_v2.0.2) and exits.

-

  **--show\_full\_usage\_info** show the many many more options available for running Trinity (expert usage).

## EXAMPLES

A typical Trinity command might be:

-

  Trinity **--seqType** fq **--max\_memory** 50G **--left** reads\_1.fq  **--right** reads\_2.fq **--CPU** 6

and for Genome-guided Trinity:

-

  Trinity **--genome\_guided\_bam** rnaseq\_alignments.csorted.bam **--max\_memory** 50G\
           **--genome\_guided\_max\_intron** 10000 **--CPU** 6

## SEE ALSO

see: /usr/lib/trinityrnaseq/sample\_data/test\_Trinity\_Assembly/ for sample data and 'runMe.sh' for example Trinity execution

For more details, visit: http://trinityrnaseq.github.io