Obitools eDNA metabarcoding
Version 1

Workflow Type: Galaxy
Stable

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Metabarcoding/eDNA through Obitools" .

This workflow allows to analyze DNA metabarcoding / eDNA data produced on Illumina sequencers using the OBITools.

Inputs

ID Name Description Type
wolf_tutorial.zip?download=1 wolf_tutorial.zip?download=1 n/a
  • File

Steps

ID Name Description
1 Illuminapairedend toolshed.g2.bx.psu.edu/repos/iuc/obi_illumina_pairend/obi_illumina_pairend/1.2.13
2 Unzip toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/0.2
3 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
4 FASTQ Groomer toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5
5 obigrep toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13
6 Line/Word/Character count wc_gnu
7 Line/Word/Character count wc_gnu
8 NGSfilter toolshed.g2.bx.psu.edu/repos/iuc/obi_ngsfilter/obi_ngsfilter/1.2.13
9 obiuniq toolshed.g2.bx.psu.edu/repos/iuc/obi_uniq/obi_uniq/1.2.13
10 obiannotate toolshed.g2.bx.psu.edu/repos/iuc/obi_annotate/obi_annotate/1.2.13
11 obistat toolshed.g2.bx.psu.edu/repos/iuc/obi_stat/obi_stat/1.2.13
12 obigrep toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13
13 obigrep toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13
14 obiclean toolshed.g2.bx.psu.edu/repos/iuc/obi_clean/obi_clean/1.2.13
15 NCBI BLAST+ blastn toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0
16 Filter sequences by ID toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7
17 Filter sequences by ID toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7
18 obitab toolshed.g2.bx.psu.edu/repos/iuc/obi_tab/obi_tab/1.2.13
19 obitab toolshed.g2.bx.psu.edu/repos/iuc/obi_tab/obi_tab/1.2.13
20 Join two Datasets join1
21 Join two Datasets join1
22 Cut Cut1
23 Filter Filter1

Version History

Version 1 (earliest) Created 9th Nov 2023 at 12:41 by Yvan Le Bras

Initial commit


Open master e601ed3
help Creators and Submitter
Activity

Views: 3139   Downloads: 211   Runs: 0

Created: 9th Nov 2023 at 12:41

Annotated Properties
Topic annotations
Operation annotations
help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 37.3 KB
Powered by
(v.1.16.0-main)
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH