Workflows
What is a Workflow?Filters
Query
Created At
Updated At
Tool
Biopython1
BLAST1
BlobToolKit1
fastp1
FastQC1
gblocks1
GetOrganelle1
ggtree1
iqtree1
MAFFT1
Minimap21
MITOS1
MultiQC1
seqkit1
Snakemake1
More...
Workflow type
Snakemake1
Tag
BGE1
Biodiversity1
Bioinformatics1
BioScanEurope1
Genome assembly1
Genomics1
sequence annotation1
More...
Submitter
Oliver White1
Team
NHM Clark group1
Space
Independent Teams1
Topic annotations
Sequence annotation1
Operation annotations
Sequence annotation1
Genome assembly17
Sequencing quality control17
Variant calling12
Sequence assembly8
Expression analysis7
Variant filtering7
Annotation6
Sequence clustering6
Sequence alignment5
Taxonomic classification5
De-novo assembly4
Conversion3
Copy number variation detection3
Data retrieval3
Gene-set enrichment analysis3
Genome annotation3
Haplotype mapping3
Protein interaction network analysis3
Transcriptome assembly3
Variant classification3
Antimicrobial resistance prediction2
Calculation2
Correlation2
Differential gene expression profiling2
Gene functional annotation2
Genetic mapping2
Genome visualisation2
Indel detection2
Modelling and simulation2
Prediction and recognition2
Protein interaction network prediction2
Scaffolding2
Sequence assembly validation2
Sequence assembly visualisation2
SNP annotation2
SNP detection2
Weighted correlation network analysis2
Analysis1
Binding site prediction1
Classification1
Clustering1
Contact map calculation1
Copy number estimation1
Data handling1
Differential protein expression profiling1
Dimensionality reduction1
DNA barcoding1
Enrichment analysis1
Expression correlation analysis1
Feature extraction1
Filtering1
Format detection1
Gene expression profiling1
Genome alignment1
Genome analysis1
Genome comparison1
Global alignment1
ID mapping1
Image analysis1
Information retrieval1
k-mer counting1
Local alignment1
Mapping1
Metabolic pathway prediction1
Named-entity and concept recognition1
Network analysis1
Nucleic acid property calculation1
Operation1
Pairwise sequence alignment1
Peptide identification1
Phasing1
Phylogenetic inference1
Protein identification1
Protein-protein interaction analysis1
Read mapping1
Relation extraction1
RNA-Seq analysis1
Sequence alignment analysis (site correlation)1
Sequence contamination filtering1
Sequence cutting1
Sequence distance matrix generation1
Sequence profile generation1
Sequence trimming1
Single particle analysis1
Standardisation and normalisation1
Statistical calculation1
Structural variation detection1
Structure-based sequence alignment1
Text annotation1
Text mining1
Transcription factor binding site prediction1
Validation1
Visualisation1
More...
Maturity
Stable1
1
Workflow matching the given criteria:
(Clear all filters)
Operation annotations:
Sequence annotation1
Stable
skim2mito
skim2mito is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.
Contents
- Setup
- Example data
- Input
- Output
- Filtering contaminants
- [Assembly and ...