Fosmid assembly annotation

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fosmids
fosmids
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BejaLab's fosmid assembly and annotation pipeline

The pipeline takes the list of fosmids in fosmids.txt that contains three columns: fosmid name and left and right reads.

The pipeline will run:

  • quality trimm

Code Snippets

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shell:
    "wget -O {output} {params.url}"
SnakeMake From line 20 of workflow/Snakefile 
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shell:
    "trim_galore --paired {input} --basename {wildcards.id} --output_dir {params.dirname}"
SnakeMake Trim_Galore From line 34 of workflow/Snakefile 
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shell:
    "spades.py -t {threads} -1 {input.r1} -2 {input.r2} -o {params.dirname}"
SnakeMake SPAdes From line 49 of workflow/Snakefile 
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shell:
    "seqkit head -n1 {input} | cutadapt --times 4 --rc --report=minimal --info-file {output.info} -g file:{input.fw} -a file:{input.rv} - > {output.fasta}"
SnakeMake Cutadapt seqkit From line 62 of workflow/Snakefile 
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shell:
    "cp {input} {output}"
SnakeMake From line 70 of workflow/Snakefile 
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run:
    sets = dict(
        fasta  = { "class": "File", "location": basename(input.fasta)  },
        submol = { "class": "File", "location": basename(input.submol) }
    )
    with open(output[0], 'w') as fd:
        yaml.dump(sets, fd)
SnakeMake From line 79 of workflow/Snakefile 
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shell:
    """
    rm -r {params.dirname}
    pgap.py --debug --ignore-all-errors --report-usage-true --cpu {threads} -o {params.dirname} {input.yaml}
    """
SnakeMake From line 97 of workflow/Snakefile 
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shell:
    "perl {input.script} {input.pgap}"
SnakeMake From line 111 of workflow/Snakefile
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Free

Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/BejaLab/fosmids
Name: fosmids
Version: 1
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Copyright: Public Domain
License: None
  • Future updates

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