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ea-utils specifications


Unique identifier OMICS_01041
Name ea-utils
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


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




No version available


ea-utils citations


Multiplicity and molecular epidemiology of Plasmodium vivax and Plasmodium falciparum infections in East Africa

Malar J
PMCID: 5932820
PMID: 29720181
DOI: 10.1186/s12936-018-2337-y

[…] nstruct the most likely haplotypes within a patient while removing false haplotypes due to PCR or sequencing error []. Before running data on SeekDeep software, all paired-end reads were merged using Fastq-join software with the parameters: Number of percent maximum difference = 8, Number of minimum overlap = 30. Joined reads of each sample were grouped into different clusters after trimming of ba […]


Exposure to toxic metals triggers unique responses from the rat gut microbiota

Sci Rep
PMCID: 5919903
PMID: 29700420
DOI: 10.1038/s41598-018-24931-w
call_split See protocol

[…] ustered into operational taxonomic units (OTUs) following the standard QIIME analysis framework. First, paired-end reads were joined together with the join_paired_ends.py script from QIIME, using the fastq-join tool and the default settings. Chimeric read identification and removal was done using usearch6.1. Reads were clustered into OTUs using the pick_open_reference.py script from QIIME, which i […]


Community Development between Porphyromonas gingivalis and Candida albicans Mediated by InlJ and Als3

PMCID: 5915736
PMID: 29691333
DOI: 10.1128/mBio.00202-18
call_split See protocol

[…] with 10 cycles of PCR amplification. Paired-end sequencing of 100 bp was undertaken using a HiSeq 2500 system (Illumina) in high-output mode with Truseq v3 reagents.FASTQ data were filtered using the fastq-mcf command from the EA-UTILS suite to remove adapter sequences and low-quality bases (). Filtered data were aligned against the reference using Bowtie v.2.2.6. The resulting aligned reads were […]


Repeated evolution of self compatibility for reproductive assurance

Nat Commun
PMCID: 5915400
PMID: 29691402
DOI: 10.1038/s41467-018-04054-6

[…] te to an average of 76-fold coverage, with a minimum of 18-fold coverage in 42 out of the 57 samples. Adapters were removed using the package cutadapt (version 1.9.1), and the reads were cleaned with fastq-mcf from the package ea-utils (version 1.1.2). Reads were mapped to the mating-type region of the h90 reference (‘MTR chromosome’ in ASM294v2 assembly) using BWA (version 0.7.13) with default se […]


Tillage Changes Vertical Distribution of Soil Bacterial and Fungal Communities

Front Microbiol
PMCID: 5900040
PMID: 29686662
DOI: 10.3389/fmicb.2018.00699
call_split See protocol

[…] Ecology (QIIME) (version 1.9.1) (). The adaptor sequence, barcode, and 30 low-quality bases at the end of each read were cut off, and then the forward and reverse Illumina reads were joined using the fastq-join method () with minimum overlap of 20 bp and maximum allowed 10% mismatches within overlap region. Sequences with Phred quality score <20 or length shorter than 200 bp were discarded. Chimer […]


Urea Amendment Decreases Microbial Diversity and Selects for Specific Nitrifying Strains in Eight Contrasting Agricultural Soils

Front Microbiol
PMCID: 5893814
PMID: 29670600
DOI: 10.3389/fmicb.2018.00634
call_split See protocol

[…] Sequence data were processed and analyzed using mothur ver. 1.35.1 (), and processed as described previously (). Briefly, samples were trimmed to 160 nt, paired-end joined using fastq-join software (), and trimmed for quality based on quality score (>35), homopolymer length (8 nt), ambiguous bases, and primer mismatches (2 nt). Samples were aligned against the SILVA database […]


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