All Published Workflows

4 workflows that have been reviewed and published

schneidernetseqpipeline
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Schneider NET-Seq pipeline
public

public

This pipeline is inteded for the use in the Schneider lab on UAB's Cheaha HPC cluster. It utilizes snakemake to organize and ...
BAM SAM BEDTools Cutadapt FastQC HTSeq htseqcount SAMtools Snakemake STAR
Free
15
genomics-read-pre-processing-without-downloading-f
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Genomics - Read pre-processing without downloading from SRA
public

public

Preprocessing of raw SARS-CoV-2 reads. This workflow contains an alternate starting point to avoid the data to be downloaded ...
BAM SAM fastp FastQC Galaxy Minimap2 MultiQC NanoPlot SAMtools WorkflowHub Genomics
Free
snps-and-indels-detection-using-samtools
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SNPs and INDELs detection using SAMTools.
public

public

Author: AMBARISH KUMAR er.ambarish@gmail.com ; ambari73_sit@jnu.ac.in This is a proposed standard operating procedure for ...
BAM CWL SAM SAMtools Genomics
Free
4
unicycler-assembly-and-annotation
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Unicycler assembly and annotation
public

public

This is a Galaxy workflow for the alignment and assembly of RNA-seq reads and annotation of generated transcripts. Galaxy is ...
BAM SAM hmmer antiSMASH BLAST BWA fastp Galaxy Glimmer MultiQC Picard SAMtools SRA Software Toolkit Unicycler UniProt WorkflowHub Genomics
Free