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Results for "Align"

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  • Archana Malhotra

    LAST

    LAST can: Handle big sequence data, e.g: Compare two vertebrate genomes Align billions of DNA reads to a genome Indicate the reliability of each aligned column. Use sequence quality data properly. Compare DNA to proteins, with frameshifts. Compare PSSMs to sequences Calculate th...

    Tags: LAST, Bioinformatics, Mapping, Match, Align, Sequences, Compare

    2962 days ago

  • Bulbul

    LAST

    LAST can: Handle big sequence data, e.g: Compare two vertebrate genomes Align billions of DNA reads to a genome Indicate the reliability of each aligned column. Use sequence quality data properly. Compare DNA to proteins, with frameshifts. Compare PSSMs to ...

    Tags: Bioinformatics, Chromosome, Genome, NGS, Align, Compare, Similarity

    2677 days ago

  • Bulbul

    pyScaf

    pyScaf orders contigs from genome assemblies utilising several types of information: paired-end (PE) and/or mate-pair libraries (NGS-based mode) long reads (NGS-based mode) synteny to the genome of some related species (reference-based mode) Scaffolding  In reference-based mode, pyS...

    Tags: Bioinformatics, Chromosome, Genome, NGS, Align, Compare, Similarity, Scaffolding

    2677 days ago

  • Archana Malhotra

    Pacbio Long Reads Compatible Software and Tools

    The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual project sites for up-to-date license information. A se...

    Tags: Bioinformatics, Chromosome, Genome, NGS, Align, LongReads, LR, Reads, Pacbio

    2591 days ago

  • Neelam Jha

    Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

    Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence in targeted regions. Consed is compatible wi...

    Tags: Consed, Finishing, Package, BAM, Viewer, Assembly, Editor, Autofinish, Autoreport, Autoedit, Align, Reads, Reference, Sequence

    1532 days ago

  • Jit

    NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore

    CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware...

    Tags: NGMLR, long-read, mapper, designed, align, PacBio, Oxford, Nanopore

    2186 days ago

  • BioStar

    PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

    Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via: sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config On MacOS, the Apple Developer tools and Fink (or MacPorts or Brew) must...

    Tags: PANDASEQ, program, align, Illumina, reads, PCR, primers, sequence, reconstruct, overlapping, sequence

    2036 days ago

  • Rahul Nayak

    VCF Compare !

    compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep sequencing platform <ftp://webdata:webdata@uss...

    Tags: bwa, mapping, genome, vcf, align, genome

    820 days ago

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