A Snakemake pipeline to go from raw .subreads.bam PacBio Iso-Seq to assembled mRNA isoforms (FASTA format)

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pacbio_snakemake
pacbio_snakemake
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Snakemake workflow: PacBio Iso-Seq processing pipeline

Introduction

A Snakemake workflow for processing PacBio raw subreads.bam into polished mRNA isoforms in FASTA format.
Optionnally, long assembled mRNAs can be al

Code Snippets

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shell:
    "ccs "
    "--min-rq {params.min_accuracy} "       # minimum predicted accuracy 
    "--report-file {params.report_file} "
    "--num-threads {threads} "   
    "{input.subreads} {output.css}"
SnakeMake From line 95 of workflow/Snakefile 
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shell:
    "lima "
    "--isoseq "
    "--peek-guess "                     # remove spurious false positive
    "--num-threads {threads} "
    "--log-file  {params.report_file} " # Split output by resolved barcode pair name.
    "{input} "
    "{params.barcodes} "
    "{params.temp_filename}"
SnakeMake MLM From line 116 of workflow/Snakefile 
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shell:
    "isoseq3 refine "
    "--require-polya "
    "--num-threads {threads} "
    " --log-file {params.report_file} "
    "{input} "
    "{params.barcodes} "
    "{output} "
SnakeMake IsoSeq3 From line 139 of workflow/Snakefile 
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shell:
    "isoseq3 cluster "
    "--num-threads {threads} "
    " --log-file {params.report_file} "
    "--verbose "
    "{input} "
    "{output} "
SnakeMake IsoSeq3 From line 160 of workflow/Snakefile 
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shell:
    "samtools fasta -o {output} {input}"
SnakeMake SAMtools From line 181 of workflow/Snakefile 
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shell:
    "pbmm2 index "
    "--num-threads {threads} "
    "--preset ISOSEQ "
    "{input} "
    "{output}"
SnakeMake pbmm2 From line 195 of workflow/Snakefile 
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shell:
    "pbmm2 align "
    "--preset ISOSEQ " 
    "--sort "
    "--num-threads {threads} "
    "{input.genome_index} "
    "{input.transcripts} "
    "{output}"
SnakeMake pbmm2 From line 213 of workflow/Snakefile 
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shell:
    "isoseq3 collapse "
    "--min-aln-coverage {params.min_aln_coverage} "
    "--min-aln-identity {params.min_aln_identity} "
    "--max-fuzzy-junction {params.max_fuzzy_junction} "
    "{input.aln} "
    "{input.css} "
    "{output.gff};"
    "mv {params.temp_fasta} {output.fasta} "
SnakeMake IsoSeq3 From line 238 of workflow/Snakefile 
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shell:
    "gffread {input} -T -o {output}"
SnakeMake gffread From line 257 of workflow/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/SilkeAllmannLab/pacbio_snakemake
Name: pacbio_snakemake
Version: v0.1.0
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Copyright: Public Domain
License: MIT License
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