ea-utils specifications

Information


Unique identifier OMICS_01041
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM, BAM, VCF, BED, FASTQ, GFF
Output format SAM, BAM, VCF, BED, FASTQ, GFF
Biological technology Illumina
Operating system Unix/Linux
Programming languages C, C++, Perl, Shell (Bash)
License MIT License
Computer skills Advanced
Version 1.04.807
Stability Stable
Source code URL https://codeload.github.com/ExpressionAnalysis/ea-utils/legacy.tar.gz/master
Maintained Yes

Subtools


  • fastq-mcf
  • fastq-multx
  • varcall
  • fastq-join

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Documentation


ea-utils citations

 (13)
2017
PMCID: 5736797

[…] on a 150-nt paired-end run of the illumina hiseq 4000 platform, with a target number of reads per library of ∼50 million. demultiplexing and read binning were performed using the open source tool fastqmultx (75)., demultiplexed illumina reads were trimmed of flanking adapter and transposon sequences using the open source tool cutadapt (76). gbs-specific sequences that were <12 nt or >25 […]

2017
PMCID: 5765365

[…] sciences core laboratories center in april 2012., initial quality filtering and barcode removal were performed by the genomics facility at cornell university’s institute of biotechnology. we used fastq-mcf (https://github.com/expressionanalysis/ea-utils/blob/wiki/fastqmcf.md) to remove illumina adaptors, trim low-quality terminal ends, discard short sequences, and filter reads with phred […]

2017
PMCID: 5645309

[…] correct orientation were selected. adapter sequences, bait sequences up to but excluding the digestion site, and bases with a phred quality score under 20 were then trimmed from the reads, using the fastq-multx, fastq-mcf and cleanadaptors v1.24 tools42,43. quality of reads was assessed using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)44., reads with a minimum length of 30  […]

2017
PMCID: 5281551

[…] quality trimming, a total of 20,746,664 and 18,145,720 reads were obtained for total rna and mrna-enriched rna samples, respectively (supplementary table s8). paired-end reads were merged using the fastq-join program 4 with default parameters. ribosomal rna (5s, 5.8s, 16s, 18s, 23s, and 28s) were identified from merged reads using sortmerna 2.0 (kopylova et al., 2012) (rrid:scr_014402) […]

2016
PMCID: 5105290

[…] de, usa) to generate approximately 13 million 101-nucleotide paired-end reads per sample. forward reads were trimmed and quality filtered using ea-utils (https://expressionanalysis.github.io/ea-utils/) and high quality reads of at least 75 nucleotides in length were mapped to the a. glabripennis reference genome assembly using tophat [70]. read counts that mapped to each locus (version […]

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