Results for "Pipeline"

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  • NCBI Prokaryotic Genome Annotation Pipeline

    NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids). Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, sma...

    Tags: Bioinformatics, Analysis, Assembly, Genome, Annotation, NCBI, Pipeline, Prokaryotes

    2509 days ago

  • TULIP - The Uncorrected Long read Itegration Pipeline

    #Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel) TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likely to follow.&...

    Tags: TULIP, Uncorrected, Long, read, Itegration, Pipeline

    2318 days ago

  • dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements

    dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not requ...

    Tags: dnaPipeTE, de-novo, assembly, annotation, Pipeline, Transposable, Elements

    2308 days ago

  • 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

    2145 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

    2018 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

    1929 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

    1893 days ago

  • Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies

    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

    1672 days ago

  • Environmental Genomics Group SciLifeLab/KTH Stockholm

    Useful Metagenomics resources

    Tags: metagenome, Genome, Resource, Pipeline

    484 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

    37 days ago