Results for "Pacbio"
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This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you get started with your data processing, as well as...Tags: Bioinformatics, Analysis, Assembly, Genome, PacBio, LongReads, Reads
2617 days ago
FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads
FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.Tags: Bioinformatics, Analysis, Assembly, Genome, PacBio, Long, FinisherSC
2614 days ago
PBSuite: Software for Long-Read Sequencing Data from PacBio
PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The Paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768PBJelly is a highly autom...Tags: Bioinformatics, Analysis, Assembly, Genome, PacBio, Long, Improve, PBSuite, PBJelly, PBHoney
2614 days ago
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
2572 days ago
- DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies Our work is published in Scientific Reports: Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologi...
Tags: Bioinformatics, Analysis, Assembly, Genome, PacBio, Long, DBG2OLC
2563 days ago
npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It also facilitates the real-time analysis of position...Tags: npScarf, Scaffolding, Completing, Assemblies, PacBio
2529 days ago
- 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)
2326 days ago
proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
proovread : large-scale high-accuracy PacBio correction through iterative short read consensus outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity (http://dx.doi.org/10.1093/bioinformatics/btu392) is easy to install/run/configure supports various types of dat HiSeq/...Tags: proovread, large-scale, high-accuracy, PacBio, correction, iterative, read, consensus
2302 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware...Tags: NGMLR, long-read, mapper, designed, align, PacBio, Oxford, Nanopore
2192 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
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 find the overlaps between reads and does not require them to be error-corrected. After the initial assembly, Flye performs an extra repe...Tags: Flye, de novo, assembler, ONT, Nanopore, PacBio, Assembly, single, molecule, sequencing, reads
2183 days ago
