ea-utils protocols

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chevron_left File format conversion SNP/SNV annotation Adapter trimming Demultiplexing Read elongation chevron_right
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ea-utils specifications

Information


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

Subtools


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

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Documentation


ea-utils in pipelines

 (103)
2018
PMCID: 5841359
PMID: 29515151
DOI: 10.1038/s41598-018-22408-4

[…] call output (bcl) obtained from the miseq were converted, but not demultiplexed, to paired-end fastq files using casava. the resulting paired-end fastq files were joined into single-end reads using fastq-join,. quality filtering was applied to the output of fastq-join requiring that greater than 80% of the base pairs be specified with a quality score of at least 25 for a read to be retained. […]

2018
PMCID: 5854365
PMID: 29543879
DOI: 10.1371/journal.pone.0194404

[…] basespace using msr v2.4 software. the remaining analyses were conducted in qiime 1.9.1 []. in total, 1,361,167 paired-end reads were generated (). paired-end reads were merged according to the fastq-join method [] using default parameters. merged reads containing ambiguous (‘n’ characters) and low-quality base calls (phred score <30) were removed. chimeric sequences were identified […]

2018
PMCID: 5859661
PMID: 29554982
DOI: 10.1186/s40168-018-0434-3

[…] seqtk []. reads were trimmed to remove the first 14 bases, those with phred quality < 20 from the end of reads, all reads containing any n bases and those with < 100 bases post-trimming using fastq-mcf []. where a read was discarded, its pair was also discarded., trinity v2.0.6 [] was used to produce multiple transcriptome assemblies using trimmed paired reads and default settings. […]

2018
PMCID: 5861049
PMID: 29559675
DOI: 10.1038/s41598-018-23261-1

[…] as controls., quality assessment was performed by prinseq-lite program (min_length:50; trim_qual_right:20; trim_qual_type:mean; trim_qual_window:20). r1 and r2 from sequencing where joined using fastq-join from ea-tools suite. data were obtained using an ad-hoc pipeline written in rstatistics environment and data processing was performed by qiime pipeline (version 1.9.0). chimeric sequences […]

2018
PMCID: 5915736
PMID: 29691333
DOI: 10.1128/mBio.00202-18

[…] 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 […]

ea-utils in publications

 (384)
PMCID: 5932820
PMID: 29720181
DOI: 10.1186/s12936-018-2337-y

[…] 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 […]

PMCID: 5919903
PMID: 29700420
DOI: 10.1038/s41598-018-24931-w

[…] 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, […]

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

[…] 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 […]

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

[…] 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 […]

PMCID: 5900040
PMID: 29686662
DOI: 10.3389/fmicb.2018.00699

[…] (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. […]

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