Workflow Steps and Code Snippets

141 tagged steps and code snippets that match keyword kraken2

Snakemake pipeline for detection limit test from laser-microdissected samples 

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shell:
    """
    if [[ {params.is_paired} = "True" ]] ; then
        kraken2 \
            --db {input.database} \
            --threads {threads} \
            --paired \
            --gzip-compressed \
            --output >(pigz > {output.out_gz}) \
            --report {output.report} \
            {input.forward_} \
            {input.reverse_} \
        > {log} 2>&1
    else
        kraken2 \
            --db {input.database} \
            --threads {threads} \
            --gzip-compressed \
            --output >(pigz > {output.out_gz}) \
            --report {output.report} \
            {input.forward_} \
        > {log} 2>&1
    fi
    """
SnakeMake kraken2 From line 20 of rules/kraken2.smk

Snakemake workflow: Bioinfo_Macro_Microbial_Metatranscriptomics 

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shell:
    """
    kraken2 \
        --db {input.database} \
        --threads {threads} \
        --paired \
        --gzip-compressed \
        --output >(pigz -11 > {output.out_gz}) \
        --report {output.report} \
        {input.forward_} \
        {input.reverse_} \
    > {log} 2>&1
    """
SnakeMake kraken2 From line 21 of rules/kraken2.smk 
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shell:
    """
    multiqc \
        --title kraken2 \
        --force \
        --filename kraken2 \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """
SnakeMake MultiQC kraken2 From line 85 of rules/report_step.smk

Snakemake workflow: Bioinfo_Macro_Microbial_Metatranscriptomics 

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shell:
    """
    kraken2 \
        --db {input.database} \
        --threads {threads} \
        --paired \
        --gzip-compressed \
        --output >(pigz -11 > {output.out_gz}) \
        --report {output.report} \
        {input.forward_} \
        {input.reverse_} \
    > {log} 2>&1
    """
SnakeMake kraken2 From line 21 of rules/kraken2.smk 
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shell:
    """
    multiqc \
        --title kraken2 \
        --force \
        --filename kraken2 \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """
SnakeMake MultiQC kraken2 From line 85 of rules/report_step.smk

Snakemake pipeline for detection limit test 

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shell:
    """
    if [[ {params.is_paired} = "True" ]] ; then
        kraken2 \
            --db {input.database} \
            --threads {threads} \
            --paired \
            --gzip-compressed \
            --output >(pigz > {output.out_gz}) \
            --report {output.report} \
            {input.forward_} \
            {input.reverse_} \
        > {log} 2>&1
    else
        kraken2 \
            --db {input.database} \
            --threads {threads} \
            --gzip-compressed \
            --output >(pigz > {output.out_gz}) \
            --report {output.report} \
            {input.forward_} \
        > {log} 2>&1
    fi
    """
SnakeMake kraken2 From line 20 of rules/kraken2.smk

Snakemake workflow for metagenomic analysis of rumen samples from sheep 

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shell:
    'kraken2 '
    '--use-names '
    '--db /dataset/2022-BJP-GTDB/scratch/2022-BJP-GTDB/kraken/GTDB '
    '-t {threads} '
    '--report {output.k2ReportGTDB} '
    '--report-minimizer-data '
    '{input.KDRs} > {output.k2OutputGTDB}'
SnakeMake kraken2 From line 187 of main/Snakefile

vRAPID: Virus Reference-based Assembly and Identification Pipeline 

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   shell:
      """
      echo "{params.run_ID} was run using the following versions \n" > {output.version_report}
      echo "\n Name                    Version                   Build  Channel \n SAMTOOLS: \n" &>> {output.version_report}
      conda list | grep -w "^samtools" &>> {output.version_report}

      echo "\n CUTADAPT: \n" &>> {output.version_report}
      conda list | grep -w "^cutadapt" &>> {output.version_report}

      echo "\n MINIMAP2: \n" &>> {output.version_report}
      conda list | grep -w "minimap2" &>> {output.version_report}

      echo "\n PILON: \n" &>> {output.version_report}
      conda list | grep "pilon" &>> {output.version_report}

	  echo "\n QUALIMAP: \n" &>> {output.version_report}
	  conda list | grep "qualimap" &>> {output.version_report}

	  echo "\n SHOVILL: \n" &>> {output.version_report}
	  conda list | grep "shovill" &>> {output.version_report}

	  echo "\n PROKKA: \n" &>> {output.version_report}
	  conda list | grep "prokka" &>> {output.version_report}

	  echo "\n KRAKEN2: \n" &>> {output.version_report}
	  conda list | grep "kraken2" &>> {output.version_report}

	  echo "\n PYTHON: \n" &>> {output.version_report}
	  conda list | grep "^python" &>> {output.version_report}

	  echo "\n MULTIQC: \n" &>> {output.version_report}
	  conda list | grep "multiqc" &>> {output.version_report}

	  echo "\n FASTQC: \n" &>> {output.version_report}
	  conda list | grep "fastqc" &>> {output.version_report}

	  echo "\n PICARD Alignment Sumamry Metrics: \n" &>> {output.version_report}
	  conda list | grep "picard" &>> {output.version_report}

	  echo "\n {params.run_ID} was aligned against the following reference: \n {params.reference} \n Using the following genabnk file: \n {params.genbankfile} \n " &>> {output.version_report}
	  echo "\n primer sets used were: \n (1) {params.ps1} \n (2) {params.ps2}" &>> {output.version_report} > {log.versioncheck} 2>&1
      """
SnakeMake FastQC MultiQC Picard Minimap2 kraken2 QualiMap metaprokka pilon shovill From line 231 of workflow/Snakefile

SpaceMicrobe Snakemake Workflow for 10X Visium Spatial Gene Expression Data 

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shell:
    """
    kraken2 --db {params.db} \
        --memory-mapping \
        --confidence 0.1 \
        --threads {threads} \
        --use-names \
        --gzip-compressed \
        --report-minimizer-data \
        --output {output.txt} \
        --report {output.report} \
        {input}
    """
SnakeMake kraken2 From line 291 of main/Snakefile

taxonomic_profiling_pipeline 

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shell:
    "kraken2 "
    "--db {params.db} "
    "--threads {threads} "
    "--output {output.kraken_class} "
    "--confidence {params.confidence} "
    "--minimum-base-quality {params.base_qual} "
    "--report {output.kraken_report} "
    "--paired "
    "--use-names "
    "--gzip-compressed "
    "{input.fwd} {input.rev}"
SnakeMake kraken2 From line 100 of main/Snakefile
tool / biotools

kraken2

kraken2

Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.

edam data_3494
edam format_1929
edam data_3028
URL https://ccb.jhu.edu/software/kraken2/
biotools kraken2
email [email protected]
edam operation_3460
edam format_1930
edam format_3475
GitHub DerrickWood/kraken2
URL https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual
doi 10.1101/762302
topic: Metagenomics
toolType: Command-line tool
operation: Taxonomic classification
signature: kraken2|kraken2-build
input:data: Taxonomy
input:format: TSV
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