Results for "Sequence"

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  • seqloc 0.6

    The Bio.SeqLoc modules in seqloc are designed to represent positions and locations (ranges of positions) on sequences, particularly nucleotide sequences. My original motivation for writing these packages was handing the locations of genes in eukaryotic genomes. Handle sequence locations for bioi...

    Tags: Bioinformatics, Computational Biology, Education, Sequence, Seq, Genome, View

    940 days ago

  • Platanus

    Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. The latest version is 1.2.4. To cite Platanus, please use the following: Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y,...

    Tags: Bioinformatics, NGS, Assembly, de novo, Sequence, Assembler, Heterozygous

    438 days ago

  • Andi

    This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial g...

    Tags: Bioinformatics, NGS, Sequence, Andi, Evolution, Distance, Tool

    438 days ago

  • SATSUMA : Highly sensitive whole-genome synteny alignments.

    Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does no...

    Tags: Bioinformatics, NGS, Sequence, Alignment, Synteny, Comparative genomics, Genomics

    438 days ago

  • methylKit

    methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal ...

    Tags: Bioinformatics, methylKit, Methylation, DNA, Analysis, Genome, NGS, Sequence

    417 days ago

  • Blobsplorer

    Blobsplorer is a tool for interactive visualization of assembled DNA sequence data ("contigs") derived from (often unintentionally) mixed-species pools. It allows the simultaneous display of GC content, coverage, and taxonomic annotation for collections of contigs with a view to separating out th...

    Tags: Bioinformatics, Blobsplorer, Visualization, Assembled DNA, Sequence, contigs, Species, Pools.

    406 days ago

  • Samtools Primer !!

    SAMtools: Primer / Tutorial by Ethan Cerami, Ph.D.keywords: samtools, next-gen, next-generation, sequencing, bowtie, sam, bam, primer, tutorial, how-to, introductionRevisions    1.0: May 30, 2013: First public release on biobits.org.    1.1: July 24, 2013: Updated wi...

    Tags: Bioinformatics, NGS, Sequence, Samtools, Primer, Tutorial

    397 days ago

  • Kraken: ultrafast metagenomic sequence classification using exact alignments

    Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify sm...

    Tags: Bioinformatics, Kraken, Metagenomic, Sequence, Classification, Alignments, NGS

    393 days ago

  • Kaiju

    Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein sequences. By default, Kaiju uses either the avai...

    Tags: Bioinformatics, Kaiju, Metagenomic, Sequence, Classification, Alignments, NGS

    393 days ago

  • EAGER

    The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format. ...

    Tags: Bioinformatics, Ancient, EAGER, Genome, DNA, Sequence, NGS

    226 days ago