Results for "ONT"
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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
1592 days ago
- Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively f...
Tags: Nanopore, adapters, Porechop, Clean, ONT
1549 days ago
medaka: Sequence correction provided by ONT Research
medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive w...Tags: medaka, Sequence, correction, ONT, Research, nanopore
1443 days ago
Rebaler: program for conducting reference-based assemblies using long reads.
Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the task of testing basecallers). It should in pri...Tags: Rebaler, program, conducting, reference-based, assemblies, long, reads, ont, pacbio
2052 days ago
rHAT: a seed-and-extension-based noisy long read alignment tool
rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.Tags: rHAT, seed-and-extension-based, noisy, long, read, alignment, tool, ont, pacbio
2047 days ago
HASLR: a hybrid assembler which uses both second and third generation sequencing reads
HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to othe...Tags: HASLR, hybrid, assembler, third, generation, sequencing, reads, illumina, pacbio, ont, assembly, genome
1458 days ago
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