All Published Workflows
87 workflows that have been reviewed and published
Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
Natrix is an open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
The need for a scalable, repro...
Plant genome assembly and annotation pipeline using snakemake
This Snakemake pipeline aims for plant genome assembly with HiFi data and genome annotation with RNA-Seq/IsoSeq. Modified fro...
Metagenomic Taxonomic Classification Benchmarking Workflow
Metagenomic taxonomic classification benchmarking This package is contains snakemake workflows, a jupyter notebook and a pyth...
Harmonization of AMR predictor tool outputs
hAMRonization is a project aiming at the harmonization of output file formats of antimicrobial resistance detection tools.
Th...
Workflow for identifying and classifying homologous gene/protein sequences
A nalysis of MO lecular E volution with BA tch E ntry (AMOEBAE)
is a customizable bioinformatics workflow ...
A snakemake workflow for metagenomic projects
A workflow for metagenomic projects A snakemake workflow for
paired- and/or single-end whole-genome shotgun metagenomic d...
Barrnap
prodigal
MEGAHIT
Biopython
BLAST
Bowtie 2
Centrifuge
CheckM
contigtax
Cutadapt
edgeR
eggNOG-mapper v2
FastANI
FastQC
FeatureCounts
Infernal cmscan (EBI)
kraken2
Krona
MaxBin
MetaBAT 2
metagenomeSeq
MetaPhlAn
metaspades
MultiQC
Pandas
Picard
SAMtools
seqtk
Snakemake
SortMeRNA
SqueezeMeta
Trimmomatic
Trnascan-SE
CONCOCT
common
gtdbtk
networkx
numpy
RGI
Alignment and antibody assembly pipelines for Croote et al. (Science, 2018)
Alignment and assembly workflows associated with Croote et al. (2018). These workflows were developed to analyze single human...
Bioinformatics pipeline for the analysis of amplicon sequencing data of eDNA samples from the PacMAN project
This is the bioinformatics pipeline developed for the PacMAN (Pacific Islands Marine Bioinvasions Alert Network). This pipeli...
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
A modular, flexible, and reproducible Snakemake workflow to perform k-mers-based GWAS.
Summary
Installation
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Novel insertion detection with 10X reads
Novel-X detects and genotypes novel sequence insertions in 10X sequencing dataset using non-trivial read alignment signatures...
A microbial genomic analysis pipeline used by the Djordjevic Lab
This repo contains a genomic analysis pipeline used for analysing mostly E. coli genomes, though it also sees use in anal...