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Citations for PacBio :
151 - 200 of 1293 citations since 2020
Citations are collected from bioRxiv only, the total number of publications could be much larger.
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bioRxiv - Genomics 2024Quote: ... Clustered isoforms were then collapsed using Isoseq collapse v4.0.0 (PacBio). Isoforms were annotated using Pigeon v1.2.0 (PacBio) ...
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bioRxiv - Genomics 2024Quote: Base-level CpG methylation was called using jasmine (PacBio), and the percent CpG methylation at each genomic position was identified from a pileup of reads using pb-CpG-tools (https://github.com/PacificBiosciences/pb-CpG-tools).
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bioRxiv - Genomics 2024Quote: ... Isoforms were annotated using Pigeon v1.2.0 (PacBio). Isoforms and genes with >= 35% of transcripts not assigned to a haplotype were classified as unphased.
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bioRxiv - Genomics 2024Quote: ... We aligned raw reads to each other using minimap2 (v2.1; Li (2018)) with an all-versus-all approach (using PacBio preset ava-pb and mapping option -g 5000 to set a maximum distance between seeds for overlap generation) ...
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bioRxiv - Genomics 2024Quote: ... For the sequencing of continuous long reads (CLR) using the Pacific Biosciences (PacBio) Sequel II platform ...
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bioRxiv - Evolutionary Biology 2024Quote: ... Libraries were prepared using the SMRT-bell library kit (PacBio) and sequenced in a 8M SMRT cell in a PacBio Sequel II under the CCS mode ...
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bioRxiv - Immunology 2024Quote: ... derived from PacBio sequencing data of the XBB.1.5 and JN.1 DMS libraries ...
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bioRxiv - Genetics 2024Quote: The Iso-Seq data was processed as recommended by PacBio. Circular Consensus sequence (CCS ...
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bioRxiv - Genetics 2024Quote: ... The raw BAM file with CCS reads was processed to obtain the isoforms and transcript structures using the SMRTLink version 10 pipeline from PacBio. In brief ...
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bioRxiv - Genetics 2024Quote: ... reads were obtained in BAM format and converted to fastq using the bam2fastq tool (version 1.3.0) from PacBio. A de novo assembly was generated using hifiasm v.0.15.4-r347 with default parameters ...
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bioRxiv - Genomics 2024Quote: ... It was then treated with DNA damage repair mix (PacBio) at 37°C for 60 minutes ...
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bioRxiv - Evolutionary Biology 2024Quote: ... Barcodes were aligned to the codon-variant table previously produced from PacBio long-read sequencing ...
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bioRxiv - Genomics 2024Quote: ... Small fragment DNA elimination was performed with the Circulomics short read eliminator kit (PacBio). Briefly ...
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bioRxiv - Genomics 2024Quote: ... The library was eventually prepared with the Sequel® II binding kit 3.2 (PacBio Ref. No. 102-194-100) and loaded with the diffusion loading mode with an on-plate concentration of 90 pM on the Pacific Biosciences SEQUEL IIe System using one SMRT cell ...
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bioRxiv - Genomics 2024Quote: ... a SMRTbell library was constructed with the SMRTbell® prep kit 3.0 (PacBio Ref. No. 102-141-700), following the manufacturer’s protocol ...
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bioRxiv - Genomics 2024Quote: ... Highly Accurate Single-Molecule Consensus Reads (CCS reads) were generated using the CCS v6 program of the SMRT- link package (PacBio, Menlo Park, CA, USA) with a minimum number of full-length subreads of 15 (99.95 base call accuracy).
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bioRxiv - Genomics 2024Quote: The genome sequencing data (PacBio, Illumina and HiC) of B ...
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bioRxiv - Genomics 2024Quote: Plant nuclei was isolated from ∼2 g leaf tissues ground with liquid nitrogen using the protocol provided by PacBio (PacBio, 2022), which was modified from Workman et al ...
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bioRxiv - Genomics 2024Quote: ... which was cleaned with SMRTbell® cleanup beads (PacBio Ref. No. 102158-300). Subsequently ...
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bioRxiv - Genomics 2024Quote: ... We used the Sequel II Binding Kit 2.0 (PacBio) to bind the library to polymerase and loaded libraries onto PacBio Sequel II ...
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bioRxiv - Genomics 2024Quote: ... and constructed PacBio SMRTbell library (∼20 kb) for PacBio Sequel using SMRTbell Express Template Prep Kit 2.0 (PacBio, Menlo Park, CA, USA) following the manufacturer recommended protocol ...
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bioRxiv - Microbiology 2024Quote: Raw PacBio raw subreads were processed to circular consensus sequencing (CCS) reads using ccs v6.4.0 (––min-rq 0.9) (this and all other PacBio software referenced was installed from the PacBio Bioconda packages (https://github.com/PacificBiosciences/pbbioconda ...
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bioRxiv - Microbiology 2024Quote: ... PN 101-763-800 Version 02) using the SMRTbell Express Template Prep kit 2.0 (PacBio). The individual libraries were barcoded using the Iso-Seq Express Oligo kit (Pacbio PN 101-737-500) ...
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bioRxiv - Genomics 2024Quote: For Continuous Long Read (CLR) sequencing technology (PacBio, CA, US), 20 µg of HMW DNA was sheared to an appropriate size range (∼25-100 kb ...
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bioRxiv - Genomics 2024Quote: For Circular Consensus Sequencing (CCS) sequencing technology (PacBio, CA, US), HMW DNA was sheared to an appropriate size range (∼10-30 kb ...
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bioRxiv - Genomics 2024Quote: ... implemented in SMRT Link (PacBio). Functional annotations of predicted genes were assigned using eggNOG-Mapper 2.1.8 (Huerta-Cepas et al. ...
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bioRxiv - Genomics 2024Quote: ... Transcript isoforms for each sample were generated using the Iso-Seq analysis pipeline (PacBio) implemented in SMRT Link (PacBio) ...
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bioRxiv - Genomics 2024Quote: ... Sequence data was obtained using the Sequel II system (PacBio), demultiplexed ...
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bioRxiv - Genomics 2024Quote: ... and used for library preparation according to the protocol of the ISO-Seq Express Template Preparation for Sequel and Sequel II System (PacBio). Libraries were sequenced using the Sequel II system (PacBio) ...
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bioRxiv - Genomics 2024Quote: ... and long-read sequencing libraries were prepared using the SMRTbell Express Template Prep Kit v2 with a barcoded overhang adapter kit (PacBio, CA, USA) for multiplexing ...
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bioRxiv - Genomics 2024Quote: ... and converted into HiFi reads using SMRT Link pipeline (PacBio). The HiFi reads were assembled in contig sequences using Hifiasm version 0.19.5 (Cheng et al. ...
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bioRxiv - Genomics 2024Quote: ... Only insertions supported by at least 10% of the sequencing depth (PacBio: 22X, 3+ reads; ONT: 12.5X, 2+ reads) were considered genuine insertions to minimise false-positive detection.
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bioRxiv - Genomics 2024Quote: ... or 1.5 (for mapped PacBio reads), and -g 50 (for mapped Illumina reads ...
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bioRxiv - Genomics 2024Quote: ... The final HMW DNA was eluted with 60 µL elution buffer (PacBio Ref. No. 101-633-500) and was subjected to quality control with NanoDrop™ One Microvolume UV-Vis Spectrophotometer ...
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bioRxiv - Genomics 2024Quote: ... or 0 (for mapped PacBio reads). The output files for all RNA-seq samples were converted to gff3 files using gffread v0.12.7 [45] ...
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bioRxiv - Genomics 2024Quote: ... and ligated with overhang adapters using SMRTbell Express Template Prep Kit 2.0 (PacBio) and purified with AMPure PB Beads (PacBio) ...
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bioRxiv - Genomics 2024Quote: ... and purified with AMPure PB Beads (PacBio). Individual libraries were size-selected (20 kb ...
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bioRxiv - Genomics 2024Quote: ... HiFi libraries were constructed using a SMRTbell Express Template Prep Kit 2.0 (PacBio); the resulting HiFi libraries were sequenced on a PacBio Revio instrument ...
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bioRxiv - Genomics 2024Quote: ... All cells were sequenced on the Sequel II instrument (PacBio) with 30Lh video times using version 2.0 sequencing chemistry and 2Lh pre-extension ...
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bioRxiv - Genomics 2024Quote: ... The size-selected and purified >10Lkbp fraction of libraries was used for sequencing on the Sequel II (PacBio) system.
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bioRxiv - Genomics 2024Quote: ... The sheared material was processed for SMRTbell library preparation using the Express Template Prep Kit v2 and SMRTbell Cleanup Kit v2 (PacBio). After checking for size and quantity ...
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bioRxiv - Genomics 2024Quote: We used long-read RNA-seq (PacBio Iso-Seq) data to look for evidence of expression of newly discovered low-frequency gene duplications ...
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bioRxiv - Genomics 2024Quote: ... Libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (PacBio). In brief ...
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bioRxiv - Genomics 2024Quote: ... Reads were clustered by isoform using Isoseq cluster 2 (PacBio v3.99.99) and aligned to hg38 using pbmm2 (PacBio v1.11.99 ...
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bioRxiv - Evolutionary Biology 2024Quote: ... we prepared SMRTbell libraries using the SMRTbell Barcoded Adapter Complete Prep Kit 96 (PacBio # 100-514-900) following manufacturer’s recommendations (PacBio protocol number 100-538-700-03) ...
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bioRxiv - Evolutionary Biology 2024Quote: ... we used 80 ng of each library in the end-repair/ligation reaction using barcoded adaptors from the SMRTbell barcoded adapter complete prep kit -96 (PacBio # 100-514-900). We then pooled all the barcoded libraries to be multiplexed and purified the pooled library using the AMPure PB Kit (PacBio # 100-265-900) ...
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bioRxiv - Genomics 2024Quote: ... The library was bound to polymerase using the Sequel II Binding Kit 2.0 (PacBio) and loaded onto the PacBio Sequel II ...
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bioRxiv - Evolutionary Biology 2024Quote: We aligned the resultant fasta files to the reference sequence using the program minimap2 (SMRT tools, PacBio). For subsequent analyses ...
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bioRxiv - Evolutionary Biology 2024Quote: ... following manufacturer’s recommendations (PacBio protocol number 100-538-700-03). Briefly ...
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bioRxiv - Evolutionary Biology 2024Quote: ... we performed a DNA damage repair reaction followed by exonuclease treatment (ExoIII and ExoVII) using the SMRTbell DNA Damage Repair Kit (PacBio # 100-486-900) according manufacturer’s instruction ...