Results for "Illumina"
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ONT assembly and Illumina polishing pipeline
This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem. Perform correction of contigs using p...Tags: ONT, assembly, Illumina, polishing, pipeline
2357 days ago
- BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a variant of the classical spectrum alignment algor...
Tags: BFC, standalone, high-performance, tool, correcting, sequencing, errors, Illumina, sequencing, data
2168 days ago
- Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via: sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config On MacOS, the Apple Developer tools and Fink (or MacPorts or Brew) must...
Tags: PANDASEQ, program, align, Illumina, reads, PCR, primers, sequence, reconstruct, overlapping, sequence
2055 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
1598 days ago
De novo Genome Assembly for Illumina Data
Written and maintained by Simon Gladman - Melbourne Bioinformatics (formerly VLSCI) Protocol Overview / Introduction In this protocol we discuss and outline the process of de novo assembly for small to medium sized genomes. https://www.melbournebioinformatics.org.au/tutorials/tutorials/assembl...Tags: De novo, Genome, Assembly, Illumina, Data
1569 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
1553 days ago
QuorUM: An Error Corrector for Illumina Reads
We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is efficiently implemented making use of current multi-...Tags: QuorUM, Error, Corrector, Illumina, Reads
1553 days ago
- KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per k-mer, K-mer Abundance Difference (KAD), which indi...
Tags: KAD, Assessing, genome, assemblies, K-mer, assemblies, abundance, Illumina, reads
1418 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
1464 days ago
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