All Published Workflows

17 workflows that have been reviewed and published

natrix
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Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
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Natrix is an open-source bioinformatics pipeline for the preprocessing of raw sequencing data. The need for a scalable, repro...
raw sequence reads Primer removal Quality control report dada2 BLAST cd-hit Cutadapt FastQC MultiQC Pandas PANDAseq seqtk ShortRead Snakemake Swarm VSEARCH AmpliconDuo data.table ggplot2 xtable dinopy numpy PyYAML tables Function analysis
Free
44
avengers-assemble
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Microbiome Analysis Workflow based on a qiime2
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This repository contains the analysis workflow for Debelius et al (doi: 10.1101/2021.03.23.436606 ). The analysis was don...
Cutadapt Pandas QIIME2.0 Snakemake VSEARCH argparser vegan numpy regex scikit-bio Function analysis
Free
46
snakemake_fastqc_mothur
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Second workflow that takes the output of the guppy workflow to run fastqc and create a multiQC report. Then run Mothur for analysis.
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This workflow takes the output from the GUPPY workflow and runs fastqc, multiqc, and mothur. Hans Vasquez-Gross Lucas...
Data Sequencing quality control Quality control report FastQC mothur MultiQC Snakemake Function analysis
Free
9
utr-variants
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Identification of 3' UTR Variants Disrupting Transcript Function Pipeline
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Identify variants occurring in 3’ UTRs that could disrupt the function of a transcript. This project involves: retrieving...
BEDTools genomepy Pandas Pybedtools Snakemake data.table ggplot2 hail numpy pysam utr-variants Function analysis
Free
21
diffparc-smk_piriform
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Diffusion-Based Parcellation of Piriform Cortex with Snakemake Workflow
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Snakemake workflow overview for diffusion-based parcellation of the piriform cortex: rule hcp7T_Diffusion_bedpostx_gpu ...
BiocSklearn C3D Greedy algorithm for Set Cover problem Pandas Singularity Hub Snakemake matplotlib nibabel numpy scipy sklearn Function analysis
Free
39
moore_upgrade
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Radiative Inclusive HLT2 Efficiency and Multiplicity Analysis Pipeline
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Repository to contain scripts used to run Moore, MooreAnalysis and DaVinci to obtain HLT2 efficiencies, extraselection multip...
Snakemake prettytable root Function analysis
Free
10
nomis_pipeline
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nomis_pipeline
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public

Repository containing workflows for IMP3 downstream analyses Related project(s): NOMIS Conda user guide ...
eukrep prodigal vcontact2 MEGAHIT antiSMASH BWA CheckM CoverM DAS Diamond Kaiju kraken2 MANTIS MaxBin MetaBAT 2 metaprokka SAMtools seqtk Snakemake SqueezeMeta subSeq CONCOCT EUKulele gtdbtk Function analysis
Free
69
macbrain-recon
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Macaque brain reconstruction snakemake workflow
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public

Macaque brain reconstruction snakemake workflow
C3D Greedy algorithm for Set Cover problem Snakemake Function analysis
Free
14
nextseq-rawdata-merge
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Workflow for merging multi-lane fastq files from the Illumina NextSeq 550 using Snakemake. In addition, basic QC and md5 checksums are generated.
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Workflow for merging multi-lane fastq files from the Illumina NextSeq 550 using Snakemake. In addition, basic QC and md5 chec...
FASTQ-illumina raw sequence reads Alignment Quality control report FastQC MultiQC Snakemake Function analysis
Free
7
metapuf
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MetaPUF
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public

No description is provided for this workflow
JSON Analysis Pandas screed SearchGUI Snakemake Function analysis metagenomics
Free
16
downstream_isoseq_process
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process aligned isoseq libraries to: 1. identify consensus gene models ; 2. compare gene model maintenance between samples
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This is a Snakemake project template. The Snakefile is under workflow . Slides describing and justifying the use ...
Gene ID Analysis Report BEDTools Biopython GenomicRanges GLUE IsoSeq3 Minimap2 orfipy Pandas SAMtools seqkit seqtk Snakemake subSeq ggplot2 tidyverse Function analysis
Free
46
genomeannotator
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Pipeline for the identification of (coding) gene structures in draft genomes.
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nf-core/genomeannotator is a bioinformatics best-practice analysis pipeline for the annotation of eukaryote genomes. It wa...
gaas spaln Exonerate MultiQC Nextflow RepeatMasker sortgrcd Function analysis Sequence analysis
Free
16