|
Genome assembly workflow for nanopore reads, for TSI |
WorkflowHub |
1114 |
https://workflowhub.eu/workflows/1114?version=1 |
Anna Syme |
tsi, genome_assembly, nanopore |
2024-09-03 |
2024-09-03 |
1 |
1 |
10.0 |
nanofilt, fastqc, porechop, bandage_image, fasta-stats, split_file_to_collection, bandage_info, flye, collapse_dataset |
Mapping assembly, De-novo assembly, Statistical calculation, Sequencing quality control, Genome assembly, Sequence composition calculation, Cross-assembly, Sequence assembly visualisation |
|
GPL-3.0-or-later |
10.48546/workflowhub.workflow.1114.1 |
Australian BioCommons, Galaxy Australia |
True |
False |
|
ERGA-BGE Genome Report ANNOT analyses |
WorkflowHub |
1096 |
https://workflowhub.eu/workflows/1096?version=2 |
Diego De Panis |
annotation, biodiversity, erga, genomics, qc |
2025-02-05 |
2025-02-24 |
2 |
2 |
13.0 |
busco, omark, lftp, pick_value, collapse_dataset, agat, tp_text_file_with_recurring_lines |
Differential protein expression profiling, Sequence assembly validation, Genome annotation, Data handling |
Genomics |
MIT |
|
ERGA Annotation |
True |
False |
|
ERGA Long reads+HiC Assembly+QC Hifiasm v2602 (WF2) |
WorkflowHub |
605 |
https://workflowhub.eu/workflows/605?version=2 |
Diego De Panis |
assembly+qc, erga, hi-c, hifi |
2026-02-11 |
2026-02-11 |
2 |
2 |
25.0 |
hifiasm, merqury, param_value_from_file, busco, bandage_image, gfa_to_fa, pick_value, gfastats |
De-novo assembly, k-mer counting, Phasing, Scaffolding, Genome assembly, Sequence assembly validation, Data handling, Sequence assembly visualisation |
Whole genome sequencing |
MIT |
|
ERGA Assembly |
True |
False |
|
ERGA Profiling Long Reads v2602 (WF1) |
WorkflowHub |
603 |
https://workflowhub.eu/workflows/603?version=2 |
Diego De Panis |
erga, profiling |
2024-09-18 |
2026-02-11 |
2 |
2 |
17.0 |
param_value_from_file, Cut1, meryl, tp_grep_tool, genomescope, tp_find_and_replace, Add_a_column1, tp_cut_tool, Convert characters1, smudgeplot |
Sequence trimming, k-mer counting, Genotyping |
Whole genome sequencing |
MIT |
|
ERGA Assembly |
True |
False |
|
ERGA DataQC HiFi v2601 (WF0) |
WorkflowHub |
602 |
https://workflowhub.eu/workflows/602?version=2 |
Diego De Panis |
dataqc, erga, hifi |
2024-09-18 |
2026-01-20 |
2 |
2 |
5.0 |
cutadapt, fastqc, seqkit_stats, multiqc, collapse_dataset |
Read pre-processing, Sequence trimming, Validation, DNA translation, Primer removal, DNA transcription, Statistical calculation, Sequencing quality control, Sequence conversion, Sequence composition calculation |
Whole genome sequencing |
MIT |
|
ERGA Assembly |
True |
False |
|
ERGA DataQC Illumina v2601 (WF0) |
WorkflowHub |
601 |
https://workflowhub.eu/workflows/601?version=2 |
Diego De Panis |
dataqc, erga, illumina |
2024-09-18 |
2026-01-20 |
2 |
2 |
7.0 |
fastqc, seqkit_stats, multiqc, __FLATTEN__, collapse_dataset, fastp |
Validation, Sequence trimming, DNA translation, DNA transcription, Statistical calculation, Sequence contamination filtering, Sequencing quality control, Sequence conversion, Sequence composition calculation |
Whole genome sequencing |
MIT |
|
ERGA Assembly |
True |
False |
|
ERGA DataQC ONT v2505 (WF0) |
WorkflowHub |
697 |
https://workflowhub.eu/workflows/697?version=1 |
Diego De Panis |
dataqc, erga, ont |
2024-01-08 |
2025-06-01 |
1 |
1 |
3.0 |
seqkit_stats, collapse_dataset, nanoplot |
DNA transcription, Box-Whisker plot plotting, Sequence conversion, Sequence trimming, DNA translation, Scatter plot plotting |
Whole genome sequencing |
MIT |
|
ERGA Assembly |
True |
False |
|
ERGA Long Reads PriAlt Purge+QC v2505 (WF3) |
WorkflowHub |
1163 |
https://workflowhub.eu/workflows/1163?version=2 |
Diego De Panis |
assembly, erga, hifi, qc |
2025-06-01 |
2025-06-01 |
2 |
2 |
25.0 |
merqury, param_value_from_file, busco, gfa_to_fa, minimap2, cat1, gfastats, purge_dups |
De-novo assembly, k-mer counting, Phasing, Scaffolding, Read binning, Pairwise sequence alignment, Genome assembly, Sequence assembly validation, Data handling |
Whole genome sequencing |
MIT |
|
ERGA Assembly |
True |
False |
|
ERGA HiC Pri Scaffolding+QC YaHS v2505 (WF4) |
WorkflowHub |
1164 |
https://workflowhub.eu/workflows/1164?version=2 |
Diego De Panis |
assembly, erga, hic, qc |
2025-02-03 |
2025-06-01 |
2 |
2 |
33.0 |
yahs, CONVERTER_fasta_to_fai, pretext_snapshot, __EXTRACT_DATASET__, pairtools_sort, bwa_mem2, param_value_from_file, Cut1, gfa_to_fa, sambamba_flagstat, pick_value, pretext_map, merqury, busco, pairtools_split, pairtools_parse, pairtools_dedup, gfastats, sambamba_merge |
De-novo assembly, k-mer counting, Phasing, Scaffolding, Sequence alignment, Genome assembly, Sequence assembly validation, Data handling |
Whole genome sequencing |
MIT |
|
ERGA Assembly |
True |
False |
|
ERGA Long reads-only Assembly+QC Hifiasm v2505 (WF2) |
WorkflowHub |
1162 |
https://workflowhub.eu/workflows/1162?version=2 |
Diego De Panis |
assembly, erga, hifi, ont, qc |
2025-05-30 |
2025-09-09 |
2 |
2 |
22.0 |
hifiasm, merqury, param_value_from_file, busco, bandage_image, gfa_to_fa, gfastats |
De-novo assembly, k-mer counting, Phasing, Scaffolding, Genome assembly, Sequence assembly validation, Data handling, Sequence assembly visualisation |
Whole genome sequencing |
MIT |
|
ERGA Assembly |
True |
False |
|
ERGA-BGE Genome Report ASM analyses (one-asm HiFi + HiC) |
WorkflowHub |
1104 |
https://workflowhub.eu/workflows/1104?version=2 |
Diego De Panis |
genome assembly, genomics, qc |
2024-11-04 |
2024-12-05 |
2 |
2 |
45.0 |
cutadapt, bg_diamond, hicexplorer_hicplotmatrix, hicexplorer_hicmergematrixbins, collapse_dataset, tp_text_file_with_recurring_lines, CONVERTER_fasta_to_fai, fasterq_dump, sam_merge2, meryl, __EXTRACT_DATASET__, __FLATTEN__, minimap2, genomescope, pairtools_sort, fastp, bwa_mem2, Cut1, datasets_download_genome, lftp, sambamba_flagstat, pick_value, blobtoolkit, rseqc_bam_stat, smudgeplot, cooler_csort_tabix, merqury, busco, pairtools_split, pairtools_parse, bedtools_makewindowsbed, pairtools_dedup, gfastats, sambamba_merge, cooler_cload_tabix |
De-novo assembly, Scaffolding, Primer removal, Sequence contamination filtering, Pairwise sequence alignment, Data deposition, Sequence assembly validation, Mapping, Data handling, Sequence alignment analysis, Visualisation, Sequence database search, k-mer counting, Phasing, Read pre-processing, Sequence trimming, Sequencing quality control, Genotyping, Data retrieval, Sequence alignment, Genome assembly, Data parsing |
Genomics |
MIT |
|
ERGA Assembly |
True |
False |
|
ERGA HiC Collapsed Scaffolding+QC YaHS v2311 (WF4) |
WorkflowHub |
702 |
https://workflowhub.eu/workflows/702?version=1 |
Diego De Panis |
erga, hic, name:assembly+qc |
2024-01-09 |
2024-01-09 |
1 |
1 |
16.0 |
bwa_mem2, pretext_snapshot, merqury, yahs, param_value_from_file, busco, bellerophon, gfa_to_fa, gfastats, pretext_map |
De-novo assembly, k-mer counting, Phasing, Scaffolding, Sequence alignment, Genome assembly, Sequence assembly validation, Data handling |
Whole genome sequencing |
MIT |
|
ERGA Assembly |
True |
False |
|
ERGA ONT+Illumina Collapsed Purge+QC v2311 (WF3) |
WorkflowHub |
701 |
https://workflowhub.eu/workflows/701?version=1 |
Diego De Panis |
erga, illumina, name:assembly+qc |
2024-01-09 |
2024-01-09 |
1 |
1 |
14.0 |
merqury, param_value_from_file, busco, gfa_to_fa, minimap2, gfastats, purge_dups |
De-novo assembly, k-mer counting, Phasing, Scaffolding, Read binning, Pairwise sequence alignment, Genome assembly, Sequence assembly validation, Data handling |
Whole genome sequencing |
MIT |
|
ERGA Assembly |
True |
False |
|
ERGA HiC Hap1Hap2 Scaffolding+QC YaHS v2309 (WF4) |
WorkflowHub |
608 |
https://workflowhub.eu/workflows/608?version=1 |
Diego De Panis |
assembly+qc, erga, hi-c |
2023-10-11 |
2024-03-13 |
1 |
1 |
30.0 |
bwa_mem2, pretext_snapshot, merqury, yahs, param_value_from_file, busco, bellerophon, gfa_to_fa, gfastats, pretext_map |
De-novo assembly, k-mer counting, Phasing, Scaffolding, Sequence alignment, Genome assembly, Sequence assembly validation, Data handling |
Whole genome sequencing |
MIT |
10.48546/workflowhub.workflow.608.1 |
ERGA Assembly |
True |
False |
|
Refining Genome Annotations with Apollo (prokaryotes) |
WorkflowHub |
749 |
https://workflowhub.eu/workflows/749?version=1 |
Anthony Bretaudeau |
genome-annotation |
2024-02-14 |
2025-11-04 |
1 |
1 |
5.0 |
create_account, create_or_update, iframe, jbrowse, list_organism |
Genome visualisation |
|
CC-BY-4.0 |
10.48546/workflowhub.workflow.749.1 |
EuroScienceGateway |
True |
False |
|
GigaScience_Peptide_Annotation_demonstration_STS26T_neoantigen_candidates_workflow |
WorkflowHub |
1790 |
https://workflowhub.eu/workflows/1790?version=1 |
|
gtn, galaxy, name:neoantigen |
2025-07-07 |
2025-07-07 |
1 |
1 |
11.0 |
converting pipes to columns\nConvert characters1, pep_pointer, tab2fasta, query_tabular, regexColumn1, converting colons to columns\nConvert characters1 |
|
|
GPL-3.0-or-later |
|
Galaxy Training Network |
True |
False |
|
Workflow 'Biodiversity data exploration tuto' |
WorkflowHub |
1693 |
https://workflowhub.eu/workflows/1693?version=1 |
|
ecology, gtn, galaxy |
2025-06-02 |
2025-06-02 |
1 |
1 |
6.0 |
tool_anonymization, ecology_link_between_var, ecology_homogeneity_normality, ecology_beta_diversity, ecology_presence_abs_abund, ecology_stat_presence_abs |
|
|
CC-BY-4.0 |
|
Galaxy Training Network |
True |
False |
|
Metagenomics assembly tutorial workflow |
WorkflowHub |
1634 |
https://workflowhub.eu/workflows/1634?version=1 |
|
gtn, galaxy |
2025-06-02 |
2025-06-02 |
1 |
1 |
8.0 |
bandage_image, bandage_info, collection_column_join, megahit, metaspades, bowtie2, megahit_contig2fastg, quast |
Visualisation, Genome assembly, Sequence assembly validation, Read mapping, Sequence assembly visualisation |
|
CC-BY-4.0 |
|
Galaxy Training Network |
True |
False |
|
Genome Annotation with Prokka |
WorkflowHub |
1497 |
https://workflowhub.eu/workflows/1497?version=1 |
|
gtn, galaxy, genome-annotation |
2025-06-02 |
2025-06-02 |
1 |
1 |
2.0 |
jbrowse, prokka |
Genome annotation, Coding region prediction, Gene prediction, Genome visualisation |
|
GPL-3.0-or-later |
|
Galaxy Training Network |
True |
False |
|
ONT -- Metagenomics-Kraken2-Krona |
WorkflowHub |
53 |
https://workflowhub.eu/workflows/53?version=1 |
Milad Miladi |
ont |
2020-08-05 |
2023-02-13 |
1 |
1 |
4.0 |
taxonomy_krona_chart, kraken2, tp_replace_in_line, datamash_reverse |
Visualisation, Taxonomic classification |
|
MIT |
|
NanoGalaxy |
True |
False |
|
Biodiversity data exploration tutorial |
WorkflowHub |
656 |
https://workflowhub.eu/workflows/656?version=1 |
Yvan Le Bras, Coline Royaux, Marie Jossé |
biodiversity, ecology |
2023-11-09 |
2024-12-09 |
1 |
1 |
6.0 |
tool_anonymization, ecology_link_between_var, ecology_homogeneity_normality, ecology_beta_diversity, ecology_presence_abs_abund, ecology_stat_presence_abs |
|
Biodiversity, Ecology |
CC-BY-4.0 |
10.48546/workflowhub.workflow.656.1 |
PNDB |
True |
False |
|
Population and community metrics calculation from Biodiversity data |
WorkflowHub |
49 |
https://workflowhub.eu/workflows/49?version=2 |
Yvan Le Bras, Coline Royaux |
biodiversity, community_metrics, ecology, glm, modeling, presence_absence, species abundance, statistics |
2020-07-24 |
2024-12-09 |
2 |
1 |
4.0 |
|
|
|
MIT |
10.48546/workflowhub.workflow.49.2 |
PNDB |
True |
False |
|
Workflow CESAB Biodiversity data training 2025 - data access exercise bonus |
https://usegalaxy.eu |
39366728f462b4f1 |
https://usegalaxy.eu/published/workflow?id=39366728f462b4f1 |
|
cesab, frb, gbif, pndb, biodiversity, data, occurences, map, gis, spatial, training |
2025-11-06 |
2025-11-06 |
12 |
12 |
|
cat1, lftp, interactive_tool_jupyter_notebook, collapse_dataset, tp_text_file_with_recurring_lines, Remove beginning1 |
|
|
MIT |
|
|
True |
False |
|
Workflow CESAB Biodiversity data training 2025 - data access exercise 1 |
https://usegalaxy.eu |
a52ea1bae6683dce |
https://usegalaxy.eu/published/workflow?id=a52ea1bae6683dce |
|
cesab, frb, gbif, pndb, biodiversity, data, download, training |
2025-11-05 |
2025-11-06 |
15 |
15 |
|
lftp, collapse_dataset, tp_text_file_with_recurring_lines, interactive_tool_jupyter_notebook |
|
|
MIT |
|
|
True |
False |
|
Workflow CESAB Biodiversity data training 2025 - data access exercise 2 |
https://usegalaxy.eu |
ca0775b90e12a784 |
https://usegalaxy.eu/published/workflow?id=ca0775b90e12a784 |
|
cesab, gbif, pndb, biodiversity, data, occurences, training |
2025-11-05 |
2025-11-06 |
9 |
9 |
|
lftp, collapse_dataset, tp_text_file_with_recurring_lines, interactive_tool_jupyter_notebook |
|
|
MIT |
|
|
True |
False |
|
Obitools eDNA metabarcoding |
https://usegalaxy.eu |
afad9a17a80bb26d |
https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d |
|
ecology, biodiversity, edna |
2023-11-09 |
2025-09-12 |
1 |
1 |
|
ncbi_blastn_wrapper, wc_gnu, obi_illumina_pairend, fastqc, Cut1, obi_tab, obi_uniq, unzip, obi_annotate, obi_grep, seq_filter_by_id, join1, fastq_groomer, obi_ngsfilter, obi_stat, Filter1, obi_clean |
Statistical calculation, Sequencing quality control, Sequence analysis, Sequence composition calculation |
|
MIT |
|
|
True |
False |
|
Satellite data for biodiversity |
https://usegalaxy.eu |
1d2cd0af01a30a46 |
https://usegalaxy.eu/published/workflow?id=1d2cd0af01a30a46 |
Marie Josse |
ecology, earth-system, satellite |
2023-03-01 |
2024-05-27 |
5 |
5 |
|
srs_preprocess_s2, srs_diversity_maps, srs_spectral_indices, srs_global_indices |
|
|
MIT |
|
|
True |
False |
|
Obis biodiversity indicator on Asian pacific |
https://usegalaxy.eu |
9e05bd65faf58ab3 |
https://usegalaxy.eu/published/workflow?id=9e05bd65faf58ab3 |
|
|
2023-03-13 |
2023-11-10 |
2 |
2 |
|
tp_cut_tool, obisindicators, csv_to_tabular, Filter1 |
|
|
|
|
|
True |
False |
|
Remote sensing Sentinel 2 data analysis to produce biodiversity metrics |
https://usegalaxy.eu |
da88448ab15d167d |
https://usegalaxy.eu/published/workflow?id=da88448ab15d167d |
|
|
2023-11-09 |
2023-11-09 |
1 |
1 |
|
srs_preprocess_s2, srs_diversity_maps, srs_spectral_indices, srs_global_indices |
|
|
|
|
|
True |
False |
|
Compute and analyze biodiversity metrics with PAMPA toolsuite |
https://usegalaxy.eu |
d33ab07e4cf44f8c |
https://usegalaxy.eu/published/workflow?id=d33ab07e4cf44f8c |
|
ecology |
2021-02-24 |
2021-02-24 |
0 |
0 |
|
tp_sort_header_tool, pampa_glmsp, Count1, mergeCols1, pampa_plotglm, pampa_glmcomm, datamash_transpose, regex1, tp_cat, pampa_communitymetrics, tp_cut_tool, pampa_presabs, regexColumn1, Filter1 |
|
|
|
|
|
True |
False |
|
16S_biodiversity_BIOM |
https://usegalaxy.org.au |
ca6f29110df8dadc |
https://usegalaxy.org.au/published/workflow?id=ca6f29110df8dadc |
|
metadegalaxy |
2019-03-21 |
2021-04-01 |
9 |
9 |
|
phyloseq_richness, phyloseq_abundance, phyloseq_taxonomy, symmetricPlot, phyloseq_DESeq2, biom_add_metadata, phyloseq_net, biom_convert |
Formatting |
|
|
|
|
True |
False |
|
16S_biodiversity_for_nonoverlap_paired_end |
https://usegalaxy.org.au |
869440d35a618836 |
https://usegalaxy.org.au/published/workflow?id=869440d35a618836 |
|
metadegalaxy |
2019-03-21 |
2021-04-01 |
18 |
18 |
|
phyloseq_DESeq2, phyloseq_net, vsearch_clustering, fastqc, bwa_mem, biom_convert, vsearch_chimera_detection, Cut1, phyloseq_abundance, symmetricPlot, trimmomatic, samtools_fastx, cat_multi_datasets, picard_FilterSamReads, addValue, phyloseq_richness, uclust2otutable, vsearch_dereplication, vsearch_search, phyloseq_taxonomy, cat1, biom_add_metadata |
DNA mapping, Genome indexing, Generation, Chimera detection, Read mapping, Statistical calculation, Sequencing quality control, Sequence alignment, Sequence composition calculation, Formatting |
|
|
|
|
True |
False |
|
16S_biodiversity_for_overlap_paired_end |
https://usegalaxy.org.au |
14e80b7f9f68ec2a |
https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a |
|
metadegalaxy |
2019-03-21 |
2021-04-01 |
16 |
16 |
|
picard_MergeSamFiles, phyloseq_DESeq2, phyloseq_net, vsearch_clustering, fastqc, bwa_mem, biom_convert, vsearch_chimera_detection, Cut1, phyloseq_abundance, symmetricPlot, trimmomatic, iuc_pear, samtools_fastx, picard_FilterSamReads, addValue, phyloseq_richness, uclust2otutable, vsearch_dereplication, vsearch_search, phyloseq_taxonomy, cat1, biom_add_metadata |
DNA mapping, Sequence merging, Genome indexing, Generation, Chimera detection, Read mapping, Statistical calculation, Sequencing quality control, Sequence alignment, Sequence composition calculation, Formatting |
|
|
|
|
True |
False |