BOL

Results for "filter"

Tags

• • Jit@jit.aber

  

  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

  2602 days ago

• • Jit@jit.aber

  

  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

  2525 days ago

• • Jit@jit.aber

  

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

  Tags: Filter, reads, size

  2484 days ago

• • Jit@jit.aber

  

  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

  2151 days ago

• • Neelam Jha@neelam

  

  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

  1226 days ago

• • Jit@jit.aber

  

  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

  2099 days ago

• • Jit@jit.aber

  

  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

  1637 days ago

• • Neelam Jha@neelam

  

  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

  1461 days ago

• • Surabhi Chaudhary@surabhi

  

  What is chastity ?

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

  Tags: ngs, illumina, sequencing, filter

  1038 days ago