All Published Workflows

6 workflows that have been reviewed and published

assembly-annotation-pipeline
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Plant genome assembly and annotation pipeline using snakemake
public

public

This Snakemake pipeline aims for plant genome assembly with HiFi data and genome annotation with RNA-Seq/IsoSeq. Modified fro...
Genome index Annotation Map BEDTools BLAST fastp FastQC GFF3 Rebase gffread HISAT2 Minimap2 RepeatMasker RepeatModeler SAMtools Snakemake StringTie RNA-Seq
Free
20
phylogenomics_intro_vertebrata
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Phylogenomics tutorial based on BUSCO genes
public

public

Phylogenomics tutorial based on BUSCO genes Disclaimer To follow the demo and make the most of it, it helps if you ha...
Genome index Phylogenetic analysis Phylogenetic tree augustus clustalo raxml-ng Biopython BUSCO IQ-TREE MAFFT API (EBI) Pandas Snakemake trimAl Whole genome sequencing
Free
55
istari
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Perform error-prone data preparation for whole genome regression modeling
public

public

An awesome whole genome regression modeling pipeline This is the home of the pipeline, istari. Its long-term goals: ...
VCF Genome index Regression analysis Quality control report gatk plink2 regenie tabix BCFtools pLink Variant Effect Predictor (VEP) Whole genome sequencing
Free
9
2023-ggg298-sourmash-compare
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A simple example snakemake workflow
public

public

A simple snakemake workflow comparing three genomes. Run it like so: snakemake -j 4 --use-conda This repo provides a snakem...
Genome index Genome analysis Plot pheatmap Snakemake ggplot2 ggplotify viridis gene similarity analysis
Free
8
gen-era-toolbox
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GEN-ERA toolbox suite of Nextflow-Singularity workflows
public

public

The GEN-ERA toolbox is a suite of Nextflow-Singularity workflows designed for comparative genomics of bacteria and small euka...
Genome index Genome assembly Genome report dRep Genomics
Free
19
genomic-variants-snps-and-indels-detection-using-1
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Genomic variants - SNPs and INDELs detection using GATK4 spark based tools.
public

public

Author: AMBARISH KUMAR [email protected] & [email protected] This is a proposed standard operating procedure for...
BAM Genome index Indel detection genetic variants gatk Bowtie 2 Picard SAMtools RNA-Seq
Free
12