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Results for "Assembly"

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  • Jit

    Genome assembly algorithms http://www.nature.com/subjects/genome-assembly-algorithms #NGS #Assembly #Algorithms #Genome #Tools

    Tags: NGS, Assembly, Algorithms, Genome, Tools

    3499 days ago

  • Jitendra Narayan

    De novo genome assembly: what every biologist should know http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1935.html #NGS #Assembly #Genome #Sequencing #DeNovo

    Tags: NGS, Assembly, Genome, Sequencing, DeNovo

    3492 days ago

  • Jitendra Narayan

    An Opinionated History of Genome Assembly Algorithms http://www.homolog.us/blogs/blog/2014/02/21/opinionated-history-genome-assembly-algorithms/ #NGS #Assembly #History

    Tags: NGS, Assembly, History

    3492 days ago

  • Gudiya Pal

    Whar are N50 and L50 of a contig assembly file? How to calculate it?

    I am currently dealing with new contig assembly dataset, and bit confused about N50 and L50 stuff ....

    Tags: NGS, N50, L50, Contig, Assembly, Genome

    2989 days ago

  • Jitendra Narayan

    MAKER

    MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-ini...

    Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, MAKER, Genome, Annotation, Pipeline, NGS, Assembly

    3014 days ago

  • Jitendra Narayan

    BUSCO

    Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at http://busco.ezlab.org/

    Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, BUSCO, Genome, Annotation, Pipeline, NGS, Assembly, Orthologs

    3014 days ago

  • Jitendra Narayan

    RATT

    RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome. It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between strains and even different species, like Plasmo...

    Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, RATT, Genome, Annotation, Pipeline, NGS, Assembly

    3014 days ago

  • Jitendra Narayan

    liftover

    Convenient conversions between genome assemblie. The liftover package makes it easy to remap genomic coordinates to a different genome assembly. More at https://github.com/aaronwolen/liftover https://www.bioconductor.org/help/workflows/liftOver/

    Tags: Bioinformatics, Computational Biology, Education, liftover, N50, NGS, Assembly, Genomics

    3013 days ago

  • Jitendra Narayan

    CrossMap

    CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig,...

    Tags: Bioinformatics, Computational Biology, Education, CrossMap, N50, NGS, Assembly, Genomics

    3013 days ago

  • Rahul Nayak

    Pilon

    Pilon is a software tool which can be used to: Automatically improve draft assemblies Find variation among strains, including large event detection Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read ...

    Tags: Bioinformatics, Computational Biology, Education, Pilon, N50, NGS, Assembly, Genomics

    3013 days ago

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