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  • PacBio
    |{{#vardefine:app|pacbio}} SMRT® Analysis is PacBio's bioinformatics software suite for analyzing single molecule, real-time DN
    2 KB (250 words) - 20:10, 24 August 2022

Page text matches

  • PacBio
    |{{#vardefine:app|pacbio}} SMRT® Analysis is PacBio's bioinformatics software suite for analyzing single molecule, real-time DN
    2 KB (250 words) - 20:10, 24 August 2022
  • Pbipa
    ...ware for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies.
    2 KB (268 words) - 21:58, 27 April 2022
  • Pbpigeon
    PacBio Pigeon is a PacBio Transcript Toolkit that contains tools to classify and filter full-length t
    2 KB (275 words) - 22:37, 21 January 2024
  • SMARTdenovo
    ...ences, though a platform dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish for ONT) are still required for higher accuracy.
    2 KB (296 words) - 21:24, 6 December 2019
  • IsoSeq3
    ...a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2.
    3 KB (295 words) - 20:10, 24 August 2022
  • Lima
    ...rcode demultiplexer, is the standard tool to identify barcode sequences in PacBio single-molecule sequencing data. Starting in SMRT Link v5.1.0, it is the to
    3 KB (299 words) - 19:57, 15 August 2022
  • Cliquesnv
    Available methods: snv-pacbio, snv-illumina, snv-pacbio-vc, snv-illumina-vc
    3 KB (301 words) - 20:24, 1 May 2024
  • Inspector
    ...long read data. The input includes a contig file, long reads (PacBio CLR, PacBio HiFi, Oxford Nanopore, or mixed platform), and a reference genome (optional
    3 KB (319 words) - 18:50, 15 August 2022
  • Minimap
    ...U cores, minimap can map 1.6Gbp PacBio reads to human in 2.5 minutes, 1Gbp PacBio E. coli reads to pre-indexed 9.6Gbp bacterial genomes in 3 minutes, to pre-
    3 KB (385 words) - 19:07, 10 June 2022
  • DEXTRACTOR
    ...mbly and reconstruction from the source .bax.h5 HDF5 files produced by the PacBio original uncompressed file. In this way, users of a PacBio can keep the data needed
    3 KB (441 words) - 19:20, 10 June 2022
  • Pbsmrtpipe
    Workflow Engine for working with PacBio data.
    2 KB (239 words) - 18:05, 15 August 2022
  • RepeatAnalysis
    PacBio tools: RepeatAnalysis, AmpFreeTools, Lima
    2 KB (238 words) - 14:34, 26 August 2020
  • Pbcore
    python package for interacting with PacBio data
    2 KB (244 words) - 20:16, 12 August 2022
  • Pbalign
    pbalign maps PacBio reads to reference sequences.
    2 KB (243 words) - 20:15, 12 August 2022
  • Bax2bam
    bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format
    2 KB (253 words) - 14:05, 10 December 2019
  • Asset
    Asset can use sequencing data from four platforms (Pacbio, 10X, Bionano, HiC) to accumulate the support evidence for a de novo assemb
    2 KB (253 words) - 20:07, 15 June 2023
  • GenomicConsensus
    ...er tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.
    2 KB (256 words) - 15:05, 10 June 2022
  • LoRDEC
    Program for correcting sequencing errors in long reads (e.g., PacBio, Oxford Nanopore) using highly accurate short reads (e.g., Illumina).
    2 KB (258 words) - 13:38, 22 April 2021
  • OrganellePBA
    OrganelleRef_PBA is a script to perform a de-novo PacBio assemblies of any organelle (chloroplast or mitochondrial genomes) using se
    2 KB (258 words) - 21:22, 6 December 2019
  • Trgt
    TRGT is a tool for targeted genotyping of tandem repeats from PacBio HiFi data. In addition to the basic size genotyping, TRGT profiles sequence
    2 KB (273 words) - 14:45, 28 July 2023
  • Trvz
    ...the repeats. TRGT is a tool for targeted genotyping of tandem repeats from PacBio HiFi data. In addition to the basic size genotyping, TRGT profiles sequence
    2 KB (273 words) - 14:46, 28 July 2023
  • PB-Assembly
    pb-assembly is a collection of PacBio software including the following applications and their dependencies:
    2 KB (269 words) - 20:11, 24 August 2022
  • LINKS
    ...gh-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, another draft genomes, etc)
    2 KB (274 words) - 16:16, 10 June 2022
  • Ngmlr
    NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a f
    2 KB (279 words) - 16:24, 10 June 2022
  • SequelQC
    SequelQC is a quality check program specifically for the PacBio Sequel platform that quickly processes raw sequence data from multiple SMRT
    2 KB (280 words) - 21:24, 6 December 2019
  • Sniffles2
    ...ffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.
    2 KB (291 words) - 20:42, 12 August 2022
  • C-wap
    ...based bioinformatics pipeline for the analysis of either long-read (ONT or PacBio) or short-read (Illumina) whole genome sequencing data of DNA extracted fro
    2 KB (281 words) - 13:16, 15 August 2022
  • Trim isoseq polya
    It is primarily developed to process the "isoseq_flnc.fasta" file of PacBio Iso-Seq
    2 KB (298 words) - 15:04, 19 August 2022
  • MITObim
    ...bler, MITObim supports in principle also data from the Iontorrent, 454 and PacBio sequencing platforms.
    3 KB (301 words) - 15:20, 22 April 2020
  • Proovread
    proovread: large-scale high accuracy PacBio correction through iterative short read consensus. Hackl, T.; Hedrich, R.;
    2 KB (269 words) - 20:27, 12 August 2022
  • Unicycler
    ...functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible
    2 KB (292 words) - 21:29, 6 December 2019
  • Homopolish
    ...e polisher originally developed for Nanopore and subsequently extended for PacBio CLR. It generates a high-quality genome (>Q50) for virus, bacteria, and fun
    3 KB (298 words) - 15:54, 6 July 2022
  • LongQC
    LongQC is a tool for the data quality control of the PacBio and ONT long reads, and it has two functionalities: sample qc and platform
    2 KB (286 words) - 14:52, 12 October 2021
  • Hifiasm
    Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with
    3 KB (303 words) - 22:23, 27 August 2020
  • Wtdbg
    Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error
    3 KB (310 words) - 17:44, 22 August 2022
  • Sniffles
    Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence fro
    3 KB (305 words) - 00:03, 22 August 2022
  • FLAIR
    ...sy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.
    3 KB (305 words) - 18:34, 12 July 2023
  • Pbmm2
    ...a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted out
    3 KB (303 words) - 20:08, 31 May 2022
  • IsONclust
    isONclust is a tool for clustering either PacBio Iso-Seq reads, or Oxford Nanopore reads into clusters, where each cluster r
    3 KB (307 words) - 13:24, 19 October 2020
  • MIRA
    ...quencing data. Can use Sanger, 454, Solexa (Illumina) and IonTorrent data. PacBio: CCS and ecCLR data usable, CLR not yet. Please visit [http://sourceforge.n
    2 KB (313 words) - 20:42, 18 August 2022
  • HASLR
    ...long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as
    3 KB (315 words) - 19:53, 17 August 2020
  • Flye
    ...is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to f
    3 KB (317 words) - 21:20, 6 December 2019
  • Mitohifi
    MitoHiFi is a python workflow that assembles mitogenomes from Pacbio HiFi reads.
    3 KB (312 words) - 17:01, 21 July 2022
  • NextDenovo
    ...a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storag
    3 KB (312 words) - 18:03, 10 May 2021
  • Quickmerge
    ...na short reads are not typically considered to cover genomic regions which PacBio and ONP long reads cannot. For more details, please see the paper that desc
    3 KB (325 words) - 21:24, 6 December 2019
  • PBJelly
    (such a PacBio RS reads or long 454 reads in fasta format) to high-confidence
    3 KB (309 words) - 17:07, 21 August 2022
  • MetaMaps
    MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets.
    3 KB (322 words) - 19:25, 14 December 2021
  • SMRT-SV
    SMRT-SV calls structural variants (SVs) using long reads (PacBio RS II or Sequel). The input is an FOFN file that lists each input file (BAX
    3 KB (340 words) - 00:03, 22 August 2022
  • Talon
    ...mapped SAM files, allowing data from different sequencing platforms (i.e. PacBio and Oxford Nanopore) to be analyzed side by side.
    3 KB (321 words) - 15:13, 23 September 2022
  • Fastv
    ...tool supports both short reads (Illumina, BGI, etc.) and long reads (ONT, PacBio, etc.)
    3 KB (327 words) - 20:08, 19 April 2024

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