Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST

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Workflow Type: Galaxy

Associated Tutorial

This workflows is part of the tutorial Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST, available in the GTN

Features

Thanks to...

Tutorial Author(s): Coline Royaux

Workflow Author(s): Coline Royaux

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1287?version=1

Inputs

ID Name Description Type
H sequences (Reverse) H sequences (Reverse) n/a
  • File[]
HCOI primers HCOI primers n/a
  • File
L sequences (Forward) L sequences (Forward) n/a
  • File[]
LCOI primers LCOI primers n/a
  • File

Steps

ID Name Description
4 ab1 to FASTQ converter toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0
5 ab1 to FASTQ converter toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0
6 What's your LCOI primer sequence identifier ? toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3
7 What's your HCOI primer sequence identifier ? toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3
8 seqtk_trimfq toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1
9 seqtk_trimfq toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1
10 Degap.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0
11 Degap.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0
12 Sort collection __SORTLIST__
13 FASTQ Groomer toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5
14 Reverse-Complement toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0
15 Reverse-Complement toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0
16 Sort collection __SORTLIST__
17 seqtk_mergepe toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1
18 FASTQ Groomer toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5
19 FASTQ to Tabular toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5
20 Tabular-to-FASTA toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
21 Align sequences toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0
22 Consensus sequence from aligned FASTA toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0
23 Merge.files toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0
24 Merge.files toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0
25 Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3
26 Align sequences toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0
27 NCBI BLAST+ blastn toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2

Outputs

ID Name Description Type
_anonymous_output_1 _anonymous_output_1 n/a
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File
_anonymous_output_9 _anonymous_output_9 n/a
  • File
_anonymous_output_10 _anonymous_output_10 n/a
  • File
_anonymous_output_11 _anonymous_output_11 n/a
  • File
_anonymous_output_12 _anonymous_output_12 n/a
  • File
_anonymous_output_13 _anonymous_output_13 n/a
  • File
_anonymous_output_14 _anonymous_output_14 n/a
  • File
_anonymous_output_15 _anonymous_output_15 n/a
  • File
_anonymous_output_16 _anonymous_output_16 n/a
  • File
_anonymous_output_17 _anonymous_output_17 n/a
  • File
w_blast_output w_blast_output n/a
  • File
w_consensus_aligned_sequences w_consensus_aligned_sequences n/a
  • File

Version History

1.0 (latest) Created 16th Jul 2024 at 14:24 by Helena Rasche

Added/updated 4 files


Open master 6122661

2.0 (earliest) Created 25th Jun 2024 at 11:19 by Helena Rasche

Added/updated 4 files


Frozen 2.0 93157b5
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
seqtk
mothur
cshl_fastx_reverse_complement
QIIME
BLAST
License
MIT License
Activity

Views: 474   Downloads: 143

Created: 25th Jun 2024 at 11:19

Last updated: 25th Jun 2024 at 11:19

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