Tags: Bioinformatics, Analysis, Assembly, Genome, Multigenome, Metagenome, Filter
2606 days ago
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short (Illumina) and long (ONT and PacBio) reads. Descr...Tags: SneakySnake, Fast, Accurate, Universal, Genome, Pre-Alignment, Filter, CPUs, GPUs, FPGAs
1229 days ago
nanofilt: Filtering and trimming of long read sequencing data
Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and mapping https://github.com/wdecoster/nanofiltTags: nanofilt, filter, trim, long, read, sequencing, NGS, nanopore
2102 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of sho...Tags: Shouji, fast, efficient, pre-alignment, filter, sequence, alignment
1641 days ago
How to filter out host reads from paired-end fastq files?
How to filter out host reads from paired-end fastq files?Tags: filter, host, reads, paired-end, fastq, files
1464 days ago
Tags: ngs, illumina, sequencing, filter
1042 days ago