Workflow Steps and Code Snippets

435 tagged steps and code snippets that match keyword Bowtie

Snakemake pipeline for detection limit test from laser-microdissected samples

shell:
    """
    bowtie2-build \
        --threads {threads} \
        {params.extra} \
        {input.reference} \
        {output.mock} \
    2> {log} 1>&2
    """

SnakeMake Bowtie 2 From line 21 of rules/bowtie2_hosts.smk

shell:
    """
    bowtie2-build \
        --threads {threads} \
        {params.extra} \
        {input.reference} \
        {output.mock} \
    2> {log} 1>&2
    """

SnakeMake Bowtie 2 From line 21 of rules/bowtie2_mags.smk

Bioinfo Macro Host Genome Short Variant Discovery Workflow

shell:
    """
    bowtie2-build \
        --threads {threads} \
        {params.extra} \
        {input.reference} \
        {params.output_path} \
    2> {log} 1>&2
    """

SnakeMake Bowtie 2 From line 29 of rules/bowtie2.smk

shell:
    """
    multiqc \
        --title bowtie2 \
        --force \
        --filename bowtie2 \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC Bowtie 2 From line 61 of rules/report_step.smk

Snakemake workflow: Bioinfo_Macro_Microbial_Metatranscriptomics

shell:
    """
    bowtie2-build \
        --threads {threads} \
        {params.extra} \
        {input.reference} \
        {output.prefix} \
    2> {log} 1>&2
    """

SnakeMake Bowtie 2 From line 17 of rules/bowtie2.smk

shell:
    """
    multiqc \
        --title bowtie2 \
        --force \
        --filename bowtie2 \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC Bowtie 2 From line 133 of rules/report_step.smk

Snakemake workflow: Bioinfo_Macro_Microbial_Metatranscriptomics

shell:
    """
    bowtie2-build \
        --threads {threads} \
        {params.extra} \
        {input.reference} \
        {output.prefix} \
    2> {log} 1>&2
    """

SnakeMake Bowtie 2 From line 17 of rules/bowtie2.smk

shell:
    """
    multiqc \
        --title bowtie2 \
        --force \
        --filename bowtie2 \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC Bowtie 2 From line 133 of rules/report_step.smk

Snakemake pipeline for detection limit test

shell:
    """
    bowtie2-build \
        --threads {threads} \
        {params.extra} \
        {input.reference} \
        {output.mock} \
    2> {log} 1>&2
    """

SnakeMake Bowtie 2 From line 21 of rules/bowtie2_hosts.smk

shell:
    """
    bowtie2-build \
        --threads {threads} \
        {params.extra} \
        {input.reference} \
        {output.mock} \
    2> {log} 1>&2
    """

SnakeMake Bowtie 2 From line 21 of rules/bowtie2_mags.smk

tool / biotools

Bowtie 2

bowtie bowtie2 Bowtie

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

References: