Results for "Long"
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Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
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 correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb&n...Tags: Wtdbg2, de novo, sequence, assembler, long, noisy, reads, PacBio, Oxford, Nanopore, ONT
2026 days ago
COSINE: non-seeding method for mapping long noisy sequences
Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long reads contaminated by a high level of errors.Tags: COSINE, non-seeding, method, mapping, long, noisy, sequences
2020 days ago
Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: https://github.com/swarris/Pacasus/blob/master/vib2017.pdf. The prepint version ...Tags: Pacasus, Correction, palindromes, long, reads, PacBio, Nanopore, ngs
2003 days ago
Genome assembly tutorial "Genome Assembly for short and long reads"
In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will know: How to perform basic quality checks on the...Tags: Genome, assembly, tutorial, short, long, reads
1934 days ago
wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
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 correction and then builds the consensus from intermediate assembly output. ./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo p...Tags: wtdbg2, fuzzy, Bruijn, graph, approach, long, noisy, reads, assembly
1919 days ago
NextDenovo: string graph-based de novo assembler for TGS long reads
NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate is about 97-98%, to further improve single base ...Tags: NextDenovo, NextOmics, string, graph-based, de novo, assembler, TGS, LongReads, assembly, long, reads
1584 days ago
- The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Computational methods used by the Shasta assembler include: Using a run-length representation of the read sequence...
Tags: Shasta, long, read, genome, assembler, tools, ngs
1574 days ago
HASLR: a tool for rapid genome assembly of long sequencing reads
HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same s...Tags: HASLR, tool, rapid, genome, assembly, long, sequencing, reads
1558 days ago
Filtlong: quality filtering tool for long reads
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtlong builds into a stand-alone executable:...Tags: Filtlong, quality, filtering, tool, long, reads
1454 days ago
- HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. More at https://www.biorxiv.org/content/10.1101/2020.03.14.992248v3
Tags: HiCanu, accurate, assembly, segmental, duplications, satellites, allelic, variants, high-fidelity, long, reads
1501 days ago
