Version 1

Transcriptome assembly workflow (single-end version)


ID Name Description Type
read_files FASTQ read file(s) FASTQ file of reverse reads in Paired End mode File[]
forward_reads Paired-end read file 1 Read file 1 in FASTQ format File
end_mode read -end mode format Read -end mode format to be specify to Trimmomatic ../tools/Trimmomatic/trimmomatic-end_mode.yaml#end_mode
trimmomatic_phred quality score format Either PHRED "33" or "64" specifies the base quality encoding. Default: 64 ../tools/Trimmomatic/trimmomatic-phred.yaml#phred
trimmomatic_slidingWindow read filtering sliding window Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold. By considering multiple bases, a single poor quality base will not cause the removal of high quality data later in the read. specifies the number of bases to average across specifies the average quality required ../tools/Trimmomatic/trimmomatic-sliding_window.yaml#slidingWindow
trinity_max_mem maximum memory allocated to Trinity Suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc) provided in Gb of RAM, ie. --max_memory 10G string
trinity_cpu number of CPUs allocated number of CPUs to use, default: 2 int?
trinity_seq_type read file(s) format type of reads: (fa or fq) string
trinity_ss_lib_type Strand-specific RNA-Seq read orientation Strand-specific RNA-Seq read orientation. if paired: RF or FR, if single: F or R. (dUTP method = RF). See web documentation string


ID Name Description
generate_raw_stats Generates a QC for the provided read file(s). Provide reverse and forward read files for paired-end (PE) or a single read file for single-end (SE).
filter_reads Filtering and trimmming read file(s) Low quality trimming (low quality ends and sequences with < quality scores less than 15 over a 4 nucleotide wide window are removed)
run_assembly Runs the actual assembly provide filtered/trimmed read file(s)
generate_filtered_stats Generates a QC for the filtered read file(s). Provide filtered/trimmed read file(s)
evaluate_contigs Evaluates the contig quality. Provide the assembled contigs (FASTA file)


ID Name Description Type
raw_qc_report n/a n/a File[]
raw_html_report n/a n/a File[]
filtered_qc_report n/a n/a File[]
filtered_html_report n/a n/a File[]
trimmomatic_log_file n/a n/a File?
forward_reads_paired n/a n/a File
forward_reads_unpaired n/a n/a File?
assembly_output_dir n/a n/a Directory
assembled_contigs n/a n/a File
transrate_output_dir n/a n/a Directory
help Creators and Submitter
  • Arnaud Meng
  • Maxim Scheremetjew

Views: 257   Downloads: 8

Created: 25th Feb 2020 at 13:18

Last updated: 25th Feb 2020 at 15:17

Last used: 17th Jan 2021 at 20:32

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Version 1 Created 25th Feb 2020 at 13:18 by Finn Bacall

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