Results for "Reads"
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Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes...Tags: Flye, Fast, accurate, de novo, assembler, single, molecule, sequencing, reads, ngs, assembly
1858 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes...Tags: Fast, accurate, de novo, assembler, single, molecule, sequencing, reads
1764 days ago
- Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all the refined variants. Sometimes it is helpful to look at the polished sequence, e.g. with the IGV browser. In...
Tags: SViper, Swipe, Structural, Variants, ONT, PacBio, reads, Illumina
1595 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
1581 days ago
FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the frequency of k-mers in sequencing data and predicts t...Tags: FastGT, alignment-free, method, calling, common, SNVs, directly, raw, sequencing, reads, alignment-free
1558 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
1555 days ago
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software ...Tags: Rcorrector, efficient, accurate, error, correction, Illumina, RNA-seq, reads
1550 days ago
- The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane McCarthy) and colleagues in Pacific Biosciences (Jo...
Tags: data, reads, free, tree, assembly
1547 days ago
Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike other demultiplexers (e.g. Albacore and Porecho...Tags: Deepbinner, signal-level, demultiplexer, Oxford, Nanopore, reads, adaptor
1545 days ago
