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Editor to share with you how to download and install trinity, I believe most people do not know much about it, so share this article for your reference, I hope you can learn a lot after reading this article, let's go to know it!

Trinity Overview Trinity: transcriptome de novo assembly software developed by Broad Institute, consisting of three independent software modules: Inchworm Chrysalis and Butterfly. Three softwares deal with large-scale RNA-seq reads data in turn.

Overview of trinity

Trinity: transcriptome de novo assembly software developed by Broad Institute, composed of three independent software modules: Inchworm Chrysalis and Butterfly. Three softwares deal with large-scale RNA-seq reads data in turn.

Download and install trinity

The latest version of trinity is v2.8.5 download official website at: https://github.com/trinityrnaseq/trinityrnaseq/wiki

Decompress: tar-zxvf Trinity-v2.8.5.tar.gz

Cd trinityrnaseq-Trinity-v2.8.5

Compilation: make

Note: trinity requires version 3. 1 or above of CMake. Remember to update CMake to the latest version and add it to the environment variable.

How to use trinity

Command: Trinity.pl-- seqType fq-- JM 50G-- left reads_1.fq-- right reads_2.fq-- CPU 6

Introduction of several important parameters:

-seqType supports input data format as fq or fa

The new version of JM memory setting v2.4.0 does not have this parameter. Instead of-max_memory, during the assembly process, jellyfish is the most resource-consuming step, so this memory is mainly controlled by jellyfish.

If it is double-ended sequencing:-left is read1-- right is read2, the reads of multiple samples is separated by commas, spaces are not allowed, but older versions such as r20131110 version of reads are separated by spaces, see the help documentation of different versions of trinity

If the single-ended sequencing parameter is-- single plus the reads of multiple samples in the file is separated by commas, spaces are not allowed.

-Threads used by CPU software

-SS_lib_type RF chain specific library needs to add this parameter.

-no_run_butterfly does not perform the butterfly step and is interrupted after the completion of the Chrysalis step

-no_run_quantifygraph does not take the step of quantifygraph

-output folder of output trinity

-no_version_check does not report version information

Note: trinity supports step-by-step operation, but I don't think it is necessary, because the reason for step-by-step operation is to avoid errors in the middle, but trinity will automatically detect the previous input. If an error occurs midway, modify it and deliver it again, it will continue to run according to the original output and will not overwrite the previous results.

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