Results for "program"

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  • LoRDEC: a hybrid error correction program for long, PacBio reads

    LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read set, whose error rate is assumed to be small, and ...

    Tags: Bioinformatics, LoRDEC, Hybrid, Error, Correction, Program, Long, PacBio, Reads, Illumina

    2545 days ago

  • AVID: A Global Alignment Program

    A new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large synt...

    Tags: AVID, Global, Alignment, Program

    2501 days ago

  • BEAP: Blast Extension and Assembly Program

    The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer"...

    Tags: BEAP, Blast, Extension, Assembly, Program, Extend, Contigs, Sequence

    2118 days ago

  • FGENESH - Program for predicting multiple genes in genomic DNA sequences

    FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et al. (2002) Science 296:79) and was used to produc...

    Tags: FGENESH, Program, predicting, multiple, genes, genomic, DNA, sequences

    1926 days ago

  • GffCompare: Program for processing GTF/GFF files

    The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF).

    Tags: GffCompare, Program, processing, GTF, GFF

    1725 days ago

  • Tbl2asn: a command-line program that automates the creation of sequence records for submission to GenBank

    Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank. Additional manual editing is not required before...

    Tags: Tbl2asn, program, creation, sequence, records, submission, GenBank

    2496 days ago

  • Opera: An optimal genome scaffolding program

    Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads.An updated version called OPERA-LG has b...

    Tags: Opera, optimal, genome, scaffolding, program

    2314 days ago

  • PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change

    PATRISTICv1.0 is a java program that calculates patristic distances from large trees in a range of file formats and allows graphical and statistical interpretation of distance matrices calculated by other programs.

    Tags: PATRISTIC, program, calculate, patristic, distances

    2425 days ago

  • HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads

    HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a ...

    Tags: HISAT2, fast, sensitive, alignment, program, mapping, next-generation, sequencing, reads, tools

    2152 days ago

  • CrossMap: a program for convenient conversion of genome coordinates

    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/BigWi...

    Tags: CrossMap, program, convenient, conversion, genome, coordinates

    2129 days ago