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