Trinity - RNA-Seq De novo Assembly

       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.

       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

       Trinity - RNA-Seq De novo Assembly

       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).

       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

Trinity version: Trinity_v2.0.2                   February 2015                                       TRINITY(1)