Compression of genomic sequencing reads via hash|based ...

Compression of genomic sequencing reads via hash-based ...

HARC reorders reads approximately according to their genome position and then encodes them to remove the redundancy between consecutive reads. While reordering ...

Compression of genomic sequencing reads via hash ... - PubMed

In both cases, it achieves 1.4×-2× compression gain over state-of-the-art read compression tools for datasets containing as many as 3 billion Illumina reads.

Compression of genomic sequencing reads via hash-based ...

Compression of genomic sequencing reads via hash-based reordering: Supplementary Data. Shubham Chandak, Kedar Tatwawadi and Tsachy Weissman.

Compression of genomic sequencing reads via hash-based ...

... SPRING is based on the HARC algorithm and supports pair-preserving compression, lossless compression (with the exception of certain cases such as FASTQ/A ...

Compression of genomic sequencing reads via hash-based ...

Motivation New Generation Sequencing (NGS) technologies for genome sequencing produce large amounts of short genomic reads per experiment, which are highly ...

FQSqueezer: k-mer-based compression of sequencing data - Nature

The key observation was that if two reads originate from the close regions of a genome their minimizers are usually the same. Thus, the reads ...

PMFFRC: a large-scale genomic short reads compression optimizer ...

We employ compression ratio as the optimization objective and propose a large-scale genomic sequencing short reads data compression optimizer, ...

Reference-free lossless compression of nanopore sequencing ...

The amount of data produced by genome sequencing experiments has been growing rapidly over the past several years, making compression ...

Study on reference-based FASTQ genome sequences compression

We propose a compression scheme based on longest matching by using FMD-index to support exact match searching. At the same time, the reverse ...

[PDF] Disk-based compression of data from genome sequencing

This paper proposes overlapping reads compression with minimizers, a compression algorithm dedicated to sequencing reads (DNA only), which makes use of a ...

Genomic Data Compression - SpringerLink

In both SAM and CRAM files, reads harboring the same sequence variation are redundantly encoded due to independent encoding of each read. In order to eliminate ...

AskScience AMA Series: We're compression experts from Stanford ...

One approach is what's called reference-based compression, which starts with one human genome sequence and describes all other sequences in ...

Disk-based compression of data from genome sequencing

Most of these algorithms reorder the reads as the first step of compression. ... ... Most of these algorithms reorder the reads as the first step of compression ...

FastqZip: An Improved Reference-Based Genome Sequence Lossy ...

We reordered the reads to get a higher compression ratio. We evaluate our algorithms on five datasets and show that FastqZip can outperform the ...

SparkGC: Spark based genome compression for large collections of ...

The main task of the first-order compression is mapping the to-be-compressed sequences to the reference sequence based on the hash index, that ...

Compression of genomic sequencing data - Wikipedia

High-throughput sequencing technologies have led to a dramatic decline of genome sequencing costs and to an astonishingly rapid accumulation of genomic data ...

Genomic Data Compression - OUCI

... Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis. Bioinformatics 34:558–567 https://doi.org/10.1093/bioinformatics ...

Compression of Genomic Sequencing Data | Encyclopedia MDPI

The notion of relative compression is obvious especially in genome re-sequencing projects where the aim is to discover variations in individual ...

Compression of raw genomic data - Shubham Chandak

Weissman; Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis,. Bioinformatics 2018. 50. Page 51 ...

Efficient sequencing data compression and FPGA acceleration ...

Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis. Bioinformatics 34, 558–567. doi:10.1093 ...