Results for "Pipeline"
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Basic Structure of Snakemake Pipeline Run !
/user/snakemake-demo$ ls config.json data envs scripts slurm-240702.out Snakefile data = mock data for the snakefile to use Snakefile = name of the snakemake “formula” file Note: The default file that snakemake looks for in the current working directory is the Snakefile. ...Tags: Snakemake, Pipeline, Flow, Learn
937 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fastp) Removal of host reads (Kraken 2; optional) Variant calling Read alignment (Bowtie 2) Sort and index alignments (SAMtools) Primer sequence removal (iVar; amplicon data only) Duplicate read marking (p...Tags: assembly, pipeline, genome, illumina
880 days ago
