All Published Workflows

6 workflows that have been reviewed and published

hribo
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HRIBO: High-throughput annotation by Ribo-seq workflow for analyzing bacterial Ribo-seq data
public

public

We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of ...
Sequence Sequence annotation ORF ID gatk ucsc-bigwigtowig BEDTools Cutadapt FastQC FeatureCounts GFFutils MultiQC Picard SAMtools Snakemake wigToBigWig bacterial assembly and annotation
Free
154
lncrna-analysis
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Annotating Novel lncRNAs Using Existing Annotations: A Snakemake-Based Pipeline
public

public

A Snakemake-based pipeline to annotate novel lncRNA using existing annotation. This pipeline uses various bioinformatics tool...
Sequence annotation FastQC gffcompare gffread HISAT2 SAMtools Snakemake StringTie Trim_Galore RNA
Free
26
circrna
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circDetector (CD): circular RNAs detection and annotation workflow
public

public

circDetector (CD) is a computational tool for detecting and annotation of circular RNAs (circRNAs) from Total RNA-Seq data...
Sequence annotation Circr Consensus Pandas Pybedtools Snakemake STAR natsort networkx numpy singleton tqdm RNA
Free
25
annotate-millet-variants-snakeflow
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Variant Annotation Workflow for Pearl Millet Using Snakemake and SnpEff
public

public

This is a little Snakemake workflow to annotate some variants from pearl millet. This task came up during a bioinformatics co...
Sequence annotation BCFtools SAMtools Snakemake snpEff Genetics
Free
12
metatdenovo
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Assembly and annotation of metatranscriptomic data
public

public

nf-core/metatdenovo is a bioinformatics best-practice analysis pipeline for Assembly and annotation of metatranscriptomic ...
Sequence annotation bioawk prodigal MEGAHIT BBMap CAT Diamond eggNOG-mapper v2 FastQC FeatureCounts hmmsearch (genouest) metaprokka MultiQC Nextflow SAMtools seqtk SPAdes TransDecoder data.table dplyr dtplyr purrr readr stringr tidyr tidyverse EUKulele kofam_scan Trim_Galore Sequence assembly
Free
54
atavide
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atavide: Comprehensive Snakemake Workflow for Advanced Metagenomics Analysis and Annotation
public

public

atavide is a complete workflow for metagenomics data analysis, including QC/QA, optional host removal, assembly and cross-...
Sequence annotation turbocor MEGAHIT Bowtie 2 Flye FOCUS Kraken kraken2 MetaBAT 2 SAMtools seqtk SUPER-FOCUS TaxonKit CONCOCT singlem Metagenomic sequencing metagenomics
Free
68