TranscriptomeAssembly-wf.single-end Version 1
Download RO CrateTranscriptome assembly workflow (single-end version)
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 |
| 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? |
| assembly_output_dir | n/a | n/a | Directory |
| assembled_contigs | n/a | n/a | File |
| transrate_output_dir | n/a | n/a | Directory |
Creators and SubmitterLicense
Activity
Views: 99 Downloads: 1
Created: 25th Feb 2020 at 13:18
Last updated: 25th Feb 2020 at 15:17
Last used: 4th Aug 2020 at 22:01
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Teams: MGnify, nf-core, Workflow Hub Administration, Galaxy COVID-19, Testing
Organizations: University of Manchester
MGnify (formerly known as EBImetagenomics) is a free resource for the assembly, analysis, archiving and browsing all types of microbiome derived sequence data.
Space: This Team is not associated with a Space
Public web page: https://www.ebi.ac.uk/metagenomics/
