• SCALCE

  • Referenced in 5 articles [sw23321]
  • Consistent Encoding) is a tool for compressing FASTQ files. It is designed specifically ... Illumina-generated FASTQ files, but supports any valid FASTQ with consistent read lengths. SCALCE...
  • FastQC

  • Referenced in 8 articles [sw16946]
  • Import of data from BAM, SAM or FastQ files (any variant); Providing a quick overview...
  • FastQ Screen

  • Referenced in 1 article [sw41936]
  • FastQ Screen: A tool for multi-genome mapping and quality control. DNA sequencing analysis typically ... incorrect experimental conclusions. Consequently, we present FastQ Screen, a tool to validate the origin ... panel of reference genomes. FastQ Screen is intended to be used routinely as a quality...
  • FASTX

  • Referenced in 2 articles [sw17090]
  • Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly...
  • ntCard

  • Referenced in 2 articles [sw36895]
  • input it takes file(s) in fasta, fastq, sam, or bam formats and computes...
  • FASTdoop

  • Referenced in 1 article [sw22016]
  • library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications. Summary ... library for the management of FASTA and FASTQ files. We show that, with respect...
  • SortMeRNA

  • Referenced in 1 article [sw17152]
  • input a file of reads (fasta or fastq format) and one or multiple rRNA database...
  • STRait Razor

  • Referenced in 1 article [sw22909]
  • detect forensically-relevant STR alleles in FASTQ sequence data, based on allelic length...
  • Stampy

  • Referenced in 1 article [sw23011]
  • SNPs; Well calibrated mapping quality scores; Input: Fastq and Fasta; gzipped or plain; Output...
  • FASTAptamer

  • Referenced in 1 article [sw28242]
  • normalizes and ranks read counts in a FASTQ file, compares populations for sequence distribution, generates...
  • ToulligQC

  • Referenced in 1 article [sw28924]
  • provided and the Albacore outputted FASTQ file (to compute the sequence statistics). Flow cells...
  • BioClojure

  • Referenced in 1 article [sw34358]
  • formats, including UniProtXML, Genbank XML, FASTA and FASTQ. In addition, it provides wrappers...
  • VSEARCH

  • Referenced in 1 article [sw34388]
  • shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging...
  • GemSIM

  • Referenced in 1 article [sw34550]
  • compatible with the generic formats SAM and FASTQ (including Illumina and Roche/454). GemSIM creates...
  • ECTyper

  • Referenced in 1 article [sw35184]
  • coli. It supports both fasta (assembled) and fastq (raw reads) file formats. The tool provides...
  • DigestiFlow

  • Referenced in 1 article [sw36002]
  • DigestiFlow: from BCL to FASTQ with ease. Management of raw-sequencing data...
  • LRez

  • Referenced in 1 article [sw37883]
  • indexing and querying both BAM and FASTQ files to quickly fetch reads or alignments sharing...
  • hppRNA

  • Referenced in 0 articles [sw28869]
  • Snakemake pipeline management system. It starts from fastq files and will produce gene/isoform expression matrix...
  • DistMap

  • Referenced in 0 articles [sw34379]
  • based operating systems. It accepts reads in FASTQ format as input and provides mapped reads...
  • R

  • Referenced in 9810 articles [sw00771]
  • R is a language and environment for statistical...