TranscriptomeAssembly-wf.paired-end
Version 1

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Transcriptome assembly workflow (paired-end version)

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SEEK ID: https://dev.workflowhub.eu/workflows/29?version=1

Inputs

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
reverse_reads Paired-end read file 2 Read file 2 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

Steps

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)

Outputs

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?
reverse_reads_paired n/a n/a
  • File
reverse_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

Version History

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

Added/updated 15 files


Open master 0261543
help Creators and Submitter
Creators
Not specified
Additional credit

Arnaud Meng, Maxim Scheremetjew

Submitter
License
Apache License 2.0
Activity

Views: 1787   Downloads: 267

Created: 25th Feb 2020 at 13:18

Last updated: 25th Feb 2020 at 15:17

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