Workflow Steps and Code Snippets

898 tagged steps and code snippets that match keyword FastQC

Snakemake workflow: dna-seq-gatk-variant-calling (v2.1.1)

wrapper:
    "0.59.2/bio/fastqc"

SnakeMake FastQC From line 9 of rules/qc.smk

Snakemake workflow: dna-seq-gatk-variant-calling (v2.1.1)

wrapper:
    "0.59.2/bio/fastqc"

SnakeMake FastQC From line 9 of rules/qc.smk

Snakemake workflow: dna-seq-gatk-variant-calling (v2.1.1)

wrapper:
    "0.59.2/bio/fastqc"

SnakeMake FastQC From line 9 of rules/qc.smk

Snakemake workflow: dna-seq-gatk-variant-calling (v2.1.1)

wrapper:
    "0.59.2/bio/fastqc"

SnakeMake FastQC From line 9 of rules/qc.smk

WES analysis pipeline

shell:
    """
    tmpdir=qc/fastqc/{wildcards.patient}-{wildcards.sample_type}.tmp 
    mkdir $tmpdir 
    fastqc --outdir $tmpdir {input} 
    mv $tmpdir/{wildcards.patient}.{wildcards.sample_type}_fastqc.html {output.html} 
    mv $tmpdir/{wildcards.patient}.{wildcards.sample_type}_fastqc.zip {output.zipdata} 
    rm -r $tmpdir
    """

SnakeMake FastQC From line 178 of rules/preprocessing.smk

Snakemake pipeline for detection limit test from laser-microdissected samples

shell:
    "fastqc {input} 2> {log} 1>&2"

SnakeMake FastQC From line 12 of rules/fastqc.smk

Bioinfo Macro Host Genome Short Variant Discovery Workflow

shell:
    "fastqc {input} 2> {log} 1>&2"

SnakeMake FastQC From line 12 of rules/fastqc.smk

Repository containing bioinformatic code for macro-scale host transcriptomic data processing (v0.0.1)

shell:
    "fastqc --quiet {input} 2> {log} 1>&2"

SnakeMake FastQC From line 12 of rules/fastqc.smk

Snakemake workflow: Bioinfo_Macro_Microbial_Metatranscriptomics

shell:
    "fastqc {input} 2> {log} 1>&2"

SnakeMake FastQC From line 12 of rules/fastqc.smk

Snakemake workflow: Bioinfo_Macro_Microbial_Metatranscriptomics

shell:
    "fastqc {input} 2> {log} 1>&2"

SnakeMake FastQC From line 12 of rules/fastqc.smk

tool / biotools

FastQC

fastqc

This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.

References: