Results for "bacterial"

Tags

  • shovill: Assemble bacterial isolate genomes from Illumina paired-end reads

    Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill pr...

    Tags: shovill, Assemble, bacterial, isolate, genomes, Illumina, paired-end, reads

    1182 days ago

  • The #bacterial #DnaA-trio #replication origin element specifies single-stranded DNA initiator #binding http://www.nature.com/nature/journal/vaop/ncurrent/full/nature17962.html

    Tags: bacterial, DnaA, replication, binding

    2851 days ago

  • Beginner’s #guide to #comparative #bacterial genome #analysis using #next-generation sequence data https://microbialinformaticsj.biomedcentral.com/articles/10.1186/2042-5783-3-2

    Tags: guide, comparative, bacterial, analysis, next

    2464 days ago

  • Unicycler: Hybrid assembly pipeline for bacterial genomes

    Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible asse...

    Tags: Unicycler, Hybrid, assembly, pipeline, bacterial, genomes

    2331 days ago

  • Tools for bacterial whole genome annotation

    RAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several hours per genome but I think this is the best way to get a high quality annotation (if you have only a few genomes to annotate). Pr...

    Tags: Tools, bacterial, whole, genome, annotation, prokaryotic, genes

    2295 days ago

  • GFinisher: a new strategy to refine and finish bacterial genome assemblies

    GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar GenomeFinisher.jar \ -i target_contigs.fasta \ ...

    Tags: GFinisher, strategy, refine, finish, bacterial, genome, assemblies

    2073 days ago

  • GTDB-Tk: A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

    GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. It is computationally efficient and designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environ...

    Tags: GTDB-Tk, toolkit, assign, objective, taxonomic, classifications, bacterial, archaeal, genomes

    2046 days ago

  • ANItools web: a web tool for fast genome comparison within multiple bacterial strains

    ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you could send us the genome sequence by email. Then ...

    Tags: ANItools, web, tool, fast, genome, comparison, multiple, bacterial, strains

    1962 days ago

  • long #Pacbio sequence reads to #assemble a #bacterial genome, including correcting the assembly with short Illumina reads. http://sepsis-omics.github.io/tutorials/modules/cmdline_assembly/

    Tags: Pacbio, assemble, bacterial

    1817 days ago

  • Gepard: allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes

    Gepard (German: "cheetah", Backronym for "GEnome PAir - Rapid Dotter") allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes. Reference: Krumsiek J, Arnold R, Rattei T. Gepard: A rapid and sensitive tool for creating dotplots on genome scale. Bioinforma...

    Tags: Gepard, calculation, dotplots, sequences, chromosomes, bacterial, genomes

    1677 days ago