Results for "Reference"

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  • Bioinformatician’s Pocket Reference !!

    It is amusing how brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5 minute discussion with neighbours (unless under special circumstances!) in our own mother-tongue. Today every bioinformatician keeps more than few languages and core ...

    Tags: Bioinformatics, Computational Biology, Pocket, Reference

    1355 days ago

  • RACA: Reference-Assisted Chromosome Assembly

    Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. http://www.ncbi.nlm.nih.gov/pubmed/23307812 http://bioen-comp...

    Tags: Bioinformatics, NGS, Assembly, Reference, RACA, Reads

    687 days ago

  • mrFAST: Micro Read Fast Alignment Search Tool

    mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes ...

    Tags: Bioinformatics, FASTQ, Reads, NGS, Mapping, Alignment, Reference

    667 days ago

  • RECORD

    Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome...

    Tags: Bioinformatics, Analysis, Assembly, Genome, Reference, NGS, RECORD

    454 days ago

  • YASRA: Reference based assembler

    YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced. Mapping reads to reference genomes makes use of LASTZ (Harris et al), a pairwise sequence aligner compatible with BLASTZ....

    Tags: Bioinformatics, YASRA, Assembler, Reference, Lastz

    358 days ago

  • DIAL

    A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. Our main ...

    Tags: Bioinformatics, DIAL, Mutation, Genome, Reference, Pipeline

    358 days ago

  • kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

    Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages 9-10) in the version 3.1 User Guide. Thanks to To...

    Tags: kSNP3.0, SNP, detection, phylogenetic, analysis, genomes, alignment, reference, genome

    76 days ago

  • MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)

    MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but...

    Tags: MashMap, fast, approximate, software, mapping, long, reads, PacBio, ONT, assembly, reference, genome(s)

    72 days ago