Results for "pipeline"
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TULIP - The Uncorrected Long read Integration Pipeline
TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likely to follow. Tulipseed takes as input alignments files of long reads to sparse short seeds, and outputs a graph...Tags: TULIP, Uncorrected, Long, read, Integration, Pipeline
2166 days ago
funannotate: Eukaryotic Genome Annotation Pipeline
Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this software package was to be able to accurately and ...Tags: funannotate, Eukaryotic, Genome, Annotation, Pipeline
2039 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an issue for downstream analysis whether you're wor...Tags: Purge, Haplotigs, Pipeline, curate, heterozygous, diploid, genome, assemblies
1950 days ago
Roary: the Pan Genome Pipeline
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible ...Tags: Roary, Pan, Genome, Pipeline
1914 days ago
- Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAP
Tags: Integrative, Meta-Assembly, Pipeline, IMAP, Chromosome-level, genome, assembler, multiple, de novo, assemblies
1693 days ago
Basic Structure of Snakemake Pipeline Run !
/user/snakemake-demo$ ls config.json data envs scripts slurm-240702.out Snakefile data = mock data for the snakefile to use Snakefile = name of the snakemake “formula” file Note: The default file that snakemake looks for in the current working directory is the Snakefile. ...Tags: Snakemake, Pipeline, Flow, Learn
918 days ago
Environmental Genomics Group SciLifeLab/KTH Stockholm
Useful Metagenomics resourcesTags: metagenome, Genome, Resource, Pipeline
506 days ago
PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens
What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene a...Tags: Phylogenomic, Analysis, Pipeline, Herbarium, Specimens
58 days ago
