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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
• 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
• TGSGapCloser
  ...error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome
  3 KB (321 words) - 15:35, 20 April 2021
• BBMap
  ...ng arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and num
  3 KB (349 words) - 17:55, 10 June 2022
• Counterr
  ...general and applicable to other sequencing platforms such as Illumina and PacBio.
  3 KB (342 words) - 21:15, 6 December 2019
• Smalt
  example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger. Paired reads
  3 KB (342 words) - 17:24, 3 June 2022
• Hiphase
  HiPhase will phase variant calls made from PacBio HiFi datasets. Key features relative to other phasing tools include:
  3 KB (337 words) - 20:21, 19 March 2024
• Jasper
  ...is an efficient polishing tool for draft genomes. It uses accurate reads (PacBio HiFi or Illumina) to evaluate consensus quality and correct consensus error
  3 KB (354 words) - 16:42, 14 December 2023
• Canu
  ...Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).
  3 KB (358 words) - 14:26, 14 April 2020
• Longshot
  ...diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned
  3 KB (352 words) - 20:04, 26 July 2023
• ABruijn
  ABruijn is a ''de novo'' assembler for PacBio and Oxford Nanopore Technologies reads. The algorithm uses an A-Bruijn grap
  3 KB (354 words) - 20:09, 24 August 2022
• Svim
  ...le insertions. In our experiments on simulated data and real datasets from PacBio and Nanopore sequencing machines, SVIM reached consistently better results
  3 KB (358 words) - 17:14, 31 May 2022
• MasHmap
  ...DNA sequences. It can be useful for mapping genome assembly or long reads (PacBio/ONT) to reference genome(s). Given a minimum alignment length and an identi
  3 KB (359 words) - 17:28, 27 May 2022
• RDnaTools
  ...pipelines for working with ribosomal DNA sequence data generated with the PacBio(R) SMRT sequencing. rDnaTools works by wrapping existing tools from microbi
  3 KB (361 words) - 21:24, 6 December 2019
• WGS Assembler
  ...vised for 454 data was named CABOG (Miller 2008). The pipeline revised for PacBio/Oxford was named 'PBcR' (Berlin 2015).
  3 KB (359 words) - 20:56, 12 August 2022
• FALCON
  ...at acceptable to FALCON. If you encounterd a Fasta2DB error '<code>Line 1: Pacbio header line format error</code>' see [https://github.com/PacificBiosciences
  3 KB (395 words) - 15:19, 15 August 2022
• Saffrontree
  ...of the data. It support NGS data (such as Illumina), 3rd generation data (Pacbio/Nanopore) and assembled sequences (FASTA).
  3 KB (400 words) - 17:17, 31 May 2022
• ToFU2
  This is the developmenal (ToFU2) branch of the PacBio IsoSeq analysis
  3 KB (398 words) - 16:38, 22 August 2022
• RepeatAnalysisTools
  sequence data generated with the PacBio No-Amp Targeted Sequencing
  4 KB (430 words) - 16:55, 15 December 2022
• Clairvoyante
  ...achieved 98.65%, 92.57%, 87.26% F1 score on the whole genome, in Illumina, PacBio, and Oxford Nanopore data, respectively. Training Clairvoyante with a sampl
  4 KB (453 words) - 13:39, 15 August 2022
• Modules Basic Usage
  E.g. this command will find pbsmrtpipe, smrtsv2, and also the pacbio (smrtlink tools) module, which module spider will not find.
  5 KB (745 words) - 16:07, 13 February 2023
• Deprecation
  * pacbio - 3.1.1, 4.0.0 * wgs - 7.0.1.23-pacbio, 7.0.1.23, 8.0.r4443-pacbio, 8.0.r4443
  9 KB (946 words) - 22:32, 15 December 2022