De novo Version 1
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Workflow Type: Galaxy
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Workflow for processing amplicon pool sequencing data without reference sequence.
This workflow allows you to reconstruct a sequence from an amplicon pool without a reference sequence. To run this workflow, you need the reads from the pool library you want to analyse in FASTQ format, separated into two files: forward and reverse. You will also need the primers used during sequencing. This workflow creates one or two contigs (depending on whether your primers were used once or twice) and a metadata file containing the length of the contigs, the number of reads mapped to them, and the average, minimum, and maximum coverage depth.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| FASTQ - Forward | FASTQ - Forward | Enter the bank containing the forward reads. |
|
| FASTQ - Reverse | FASTQ - Reverse | Enter the bank containing the reverse reads. |
|
| Filter FASTQ - Maximum size | Filter FASTQ - Maximum size | Maximum reads filtering size. Leave 0 if no filtering. |
|
| Filter FASTQ - Minimum size | Filter FASTQ - Minimum size | Minimum reads filtering size. Leave 0 if no filtering. |
|
| Forward primer | Forward primer | Enter your forward primer in capital letters. |
|
| Is your primer used more than once? | Is your primer used more than once? | n/a |
|
| Reverse primer | Reverse primer | Enter your reverse primer in capital letters. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2 |
| 8 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 |
| 9 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 |
| 10 | Pear | toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.4 |
| 11 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2 |
| 12 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2 |
| 13 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2 |
| 14 | Filter FASTQ | toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2 |
| 15 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 16 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3 |
| 17 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3 |
| 18 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 |
| 19 | MEGAHIT | toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2 |
| 20 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0 |
| 21 | FASTQ to FASTA | toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2+galaxy2 |
| 22 | Chop.seqs | toolshed.g2.bx.psu.edu/repos/iuc/mothur_chop_seqs/mothur_chop_seqs/1.39.5.0 |
| 23 | cap3 | toolshed.g2.bx.psu.edu/repos/artbio/cap3/cap3/2.0.0 |
| 24 | FASTA Width | toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2 |
| 25 | Select first | Show beginning1 |
| 26 | Select first | Show beginning1 |
| 27 | Select last | Show tail1 |
| 28 | NCBI BLAST+ blastn | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.16.0+galaxy0 |
| 29 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 |
| 30 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 31 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 32 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0 |
| 33 | NCBI BLAST+ blastn | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.16.0+galaxy0 |
| 34 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 |
| 35 | Samtools fastx | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.21+galaxy0 |
| 36 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 37 | Concatenate datasets | cat1 |
| 38 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0 |
| 39 | cap3 | toolshed.g2.bx.psu.edu/repos/artbio/cap3/cap3/2.0.0 |
| 40 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 41 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0 |
| 42 | Samtools fastx | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.21+galaxy0 |
| 43 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 44 | SeqKit statistics | toolshed.g2.bx.psu.edu/repos/iuc/seqkit_stats/seqkit_stats/2.10.1+galaxy0 |
| 45 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 46 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 |
| 47 | Select last | Show tail1 |
| 48 | Concatenate datasets | cat1 |
| 49 | JBrowse2 | toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.6.5+galaxy0 |
| 50 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0 |
| 51 | Cut | Cut1 |
| 52 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 53 | Samtools idxstats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.7 |
| 54 | Samtools depth | toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.21+galaxy0 |
| 55 | cap3 | toolshed.g2.bx.psu.edu/repos/artbio/cap3/cap3/2.0.0 |
| 56 | Add line to file | toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 |
| 57 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0 |
| 58 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 59 | Select first | Show beginning1 |
| 60 | Paste | Paste1 |
| 61 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0 |
| 62 | Cut | Cut1 |
| 63 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 64 | Paste | Paste1 |
| 65 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 |
| 66 | SeqKit statistics | toolshed.g2.bx.psu.edu/repos/iuc/seqkit_stats/seqkit_stats/2.10.1+galaxy0 |
| 67 | table rename column | toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy0 |
| 68 | JBrowse2 | toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.6.5+galaxy0 |
| 69 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 70 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 71 | Paste | Paste1 |
| 72 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0 |
| 73 | Select last | Show tail1 |
| 74 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 75 | Samtools depth | toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.21+galaxy0 |
| 76 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 77 | Samtools idxstats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.7 |
| 78 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 79 | Cut | Cut1 |
| 80 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 81 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0 |
| 82 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 83 | Add line to file | toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 |
| 84 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 85 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 86 | Paste | Paste1 |
| 87 | Select first | Show beginning1 |
| 88 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 89 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 90 | Cut | Cut1 |
| 91 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 92 | Paste | Paste1 |
| 93 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 94 | table rename column | toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy0 |
| 95 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 96 | Paste | Paste1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| forward_qc | forward_qc | n/a |
|
| reverse_qc | reverse_qc | n/a |
|
| paired_qc | paired_qc | n/a |
|
| contig1 | contig1 | n/a |
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| contig2 | contig2 | n/a |
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| blastn1 | blastn1 | n/a |
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| blastn2 | blastn2 | n/a |
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| consensus_contig1 | consensus_contig1 | n/a |
|
| browser1 | browser1 | n/a |
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| consensus_contig2 | consensus_contig2 | n/a |
|
| browser2 | browser2 | n/a |
|
| metadata1 | metadata1 | n/a |
|
| metadata2 | metadata2 | n/a |
|
Version History
Version 1 (earliest) Created 16th Dec 2025 at 09:38 by Molène Mahé
Initial commit
Open
mastercc333b9
Creators and SubmitterLicense
Activity
Views: 850 Downloads: 119 Runs: 1
Created: 16th Dec 2025 at 09:38
Tags AttributionsNone
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