Nanopore Preprocessing

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Workflow Type: Galaxy

Microbiome - QC and Contamination Filtering

Associated Tutorial

This workflows is part of the tutorial Nanopore Preprocessing, available in the GTN

Features

Thanks to...

Tutorial Author(s): Bérénice Batut, Engy Nasr, Paul Zierep

Tutorial Contributor(s): Hans-Rudolf Hotz, Wolfgang Maier

Workflow Author(s): Bérénice Batut, Engy Nasr, Paul Zierep

Funder(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health, EOSC-Life

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1087?version=2

Inputs

ID Name Description Type
collection_of_all_samples collection_of_all_samples Nanopore reads of each sample are all in a single fastq or fastq.gz file
  • File[]
samples_profile samples_profile based on the lab preparation of the samples during sequencing, there should be a sample profile better than the other, to be chosen as an optional input to Minimap2. e.g. PacBio/Oxford Nanpore For more details check: https://github.com/lh3/minimap2?tab=readme-ov-file#use-cases
  • string?

Steps

ID Name Description
2 Porechop Preprocessing (Trimming) toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0
3 NanoPlot Quality Check Before Preprocessing toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1
4 FastQC Quality Check Before Preprocessing toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
5 fastp Preprocessing toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0
6 MultiQC Quality Control Before and After Preprocessing toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
7 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
8 NanoPlot Nanoplot Quality Check After Preprocessing toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1
9 FastQC Quality Check After Preprocessing toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
10 Split BAM by reads mapping status toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.2+galaxy2
11 Select Grep1
12 Samtools fastx toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.15.1+galaxy2
13 Samtools fastx toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.15.1+galaxy2
14 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
15 Filter failed datasets __FILTER_FAILED_DATASETS__
16 Kraken2 toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1
17 Cut Cut1
18 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
19 Krakentools: Extract Kraken Reads By ID toolshed.g2.bx.psu.edu/repos/iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads/1.2+galaxy1
20 Select Grep1
21 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
22 Cut Cut1
23 Column join toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3
24 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
25 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
26 MultiQC Quality Control Before and After Preprocessing toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1

Outputs

ID Name Description Type
porechop_output_trimmed_reads porechop_output_trimmed_reads n/a
  • File
nanoplot_qc_on_reads_before_preprocessing_nanostats nanoplot_qc_on_reads_before_preprocessing_nanostats n/a
  • File
nanoplot_on_reads_before_preprocessing_nanostats_post_filtering nanoplot_on_reads_before_preprocessing_nanostats_post_filtering n/a
  • File
nanoplot_qc_on_reads_before_preprocessing_html_report nanoplot_qc_on_reads_before_preprocessing_html_report n/a
  • File
fastqc_quality_check_before_preprocessing_html_file fastqc_quality_check_before_preprocessing_html_file n/a
  • File
fastqc_quality_check_before_preprocessing_text_file fastqc_quality_check_before_preprocessing_text_file n/a
  • File
nanopore_sequenced_reads_processed_with_fastp_after_host_removal nanopore_sequenced_reads_processed_with_fastp_after_host_removal n/a
  • File
nanopore_sequenced_reads_processed_with_fastp_after_host_removal_html_report nanopore_sequenced_reads_processed_with_fastp_after_host_removal_html_report n/a
  • File
multiQC_stats_before_preprocessing multiQC_stats_before_preprocessing n/a
  • File
multiQC_html_report_before_preprocessing multiQC_html_report_before_preprocessing n/a
  • File
bam_map_to_host bam_map_to_host n/a
  • File
nanoplot_qc_on_reads_after_preprocessing_html_report nanoplot_qc_on_reads_after_preprocessing_html_report n/a
  • File
nanoplot_on_reads_after_preprocessing_nanostats_post_filtering nanoplot_on_reads_after_preprocessing_nanostats_post_filtering n/a
  • File
nanoplot_qc_on_reads_after_preprocessing_nanostats nanoplot_qc_on_reads_after_preprocessing_nanostats n/a
  • File
fastqc_quality_check_after_preprocessing_text_file fastqc_quality_check_after_preprocessing_text_file n/a
  • File
fastqc_quality_check_after_preprocessing_html_file fastqc_quality_check_after_preprocessing_html_file n/a
  • File
non_host_sequences_bam non_host_sequences_bam n/a
  • File
host_sequences_bam host_sequences_bam n/a
  • File
total_sequences_before_hosts_sequences_removal total_sequences_before_hosts_sequences_removal n/a
  • File
host_sequences_fastq host_sequences_fastq n/a
  • File
non_host_sequences_fastq non_host_sequences_fastq n/a
  • File
kraken2_with_kalamri_database_output kraken2_with_kalamri_database_output n/a
  • File
kraken2_with_kalamri_database_report kraken2_with_kalamri_database_report n/a
  • File
quality_retained_all_reads quality_retained_all_reads n/a
  • File
hosts_qc_text_file hosts_qc_text_file n/a
  • File
hosts_qc_html hosts_qc_html n/a
  • File
collection_of_preprocessed_samples collection_of_preprocessed_samples n/a
  • File
total_sequences_after_hosts_sequences_removal total_sequences_after_hosts_sequences_removal n/a
  • File
quality_retained_hosts_reads quality_retained_hosts_reads n/a
  • File
removed_hosts_percentage_tabular removed_hosts_percentage_tabular n/a
  • File
multiQC_html_report_after_preprocessing multiQC_html_report_after_preprocessing n/a
  • File
multiQC_stats_after_preprocessing multiQC_stats_after_preprocessing n/a
  • File

Version History

3.0 (latest) Created 16th Jul 2024 at 14:05 by Helena Rasche

Added/updated 4 files


Open master 0a8feb6

5.0 (earliest) Created 25th Jun 2024 at 10:56 by Helena Rasche

Added/updated 4 files


Frozen 5.0 71b4f35
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
NanoPlot
FastQC
fastp
MultiQC
Minimap2
BamTools
SAMtools
kraken2
License
MIT License
Activity

Views: 552   Downloads: 186

Created: 25th Jun 2024 at 10:55

Last updated: 25th Jun 2024 at 10:56

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