Snakemake Workflow for NGS Data Analysis

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alignmentworkflow
alignmentworkflow
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This is an example workflow for analyzing NGS data. The workflow takes raw data (.fastq) and processes through the following workflow:

  1. quality assessment, filtering, trim adaptors (fastp)

  2. alignment to reference genome (bowtie2)

  3. index, sort, and binary compress reads (samtools)

This is a minor change, to include information about Snakemake!!

Code Snippets

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shell:
	"bowtie2 -x {params.bowtie_index} {input.sample} 2> {log} | samtools view -bS - -o {output.bam}"
SnakeMake SAMtools Bowtie 2 From line 16 of main/Snakefile 
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shell:
    "samtools sort {input.bam_fin} -o {output.bam_sorted}"
SnakeMake SAMtools From line 24 of main/Snakefile 
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shell:
    "samtools index {input.sorted_fin}"
SnakeMake SAMtools From line 32 of main/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/clairelundstrom/AlignmentWorkflow
Name: alignmentworkflow
Version: 1
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Copyright: Public Domain
License: None
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