Results for "Filter"

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  • Multigenome assembly

    This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gen...

    Tags: Bioinformatics, Analysis, Assembly, Genome, Multigenome, Metagenome, Filter

    2572 days ago

  • Filter #blank #lines from a #fasta file using sed. $ sed '/^$/d' finalSample.fa > finalSample_filtered.fa #Linux #Filter #FASTA #SED

    Tags: blank, lines, fasta, Linux, Filter, FASTA, SED

    2495 days ago

  • #Filter out #reads with #size to discard reads containing many Ns. BBNorm ( https://sourceforge.net/projects/bbmap/ )

    Tags: Filter, reads, size

    2454 days ago

  • reformat.sh in=reads.fq out=highQuality.fq maq=16 (that will throw away all reads with average quality below 16) #Filter #BBMap #Quality

    Tags: Filter, BBMap, Quality

    2121 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

    1195 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/nanofilt

    Tags: nanofilt, filter, trim, long, read, sequencing, NGS, nanopore

    2069 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

    1607 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

    1431 days ago

  • What is chastity ?

    While working with illumina data, I came cross chastity filter.  I am wondering about it !

    Tags: ngs, illumina, sequencing, filter

    1008 days ago