ea-utils pipeline

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

 (38)
2017
PMCID: 5281551
PMID: 28197133
DOI: 10.3389/fmicb.2017.00067

[…] 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) […]

2017
PMCID: 5345719
PMID: 28082325
DOI: 10.1534/g3.116.038190

[…] to rule out errors in data processing, we also directly analyzed alignments of reads to the nipponbare reference genome independently from our gbs pipeline. for this, reads were demultiplexed using fastq-multx (https://github.com/brwnj/fastq-multx), and aligned using bwa as described above. we then inspected read alignments from selected, error-prone markers using the r package gviz (hahne […]

2017
PMCID: 5345719
PMID: 28082325
DOI: 10.1534/g3.116.038190

[…] we also directly analyzed alignments of reads to the nipponbare reference genome independently from our gbs pipeline. for this, reads were demultiplexed using fastq-multx (https://github.com/brwnj/fastq-multx), and aligned using bwa as described above. we then inspected read alignments from selected, error-prone markers using the r package gviz (hahne and ivanek 2016). when we analyzed the 10 […]

2017
PMCID: 5429845
PMID: 28408760
DOI: 10.1038/s41598-017-00893-3

[…] and sequenced according to the illumina truseq v3 protocol on the hiseq2000 with a single read 50 bp and 7 bp index., the obtained illumina reads from the rna-sequencing were filtered using fastq mcf and aligned against the cdna sequences of s. plymythica pri-2c using bowtie 2 (2.2.5)27 with the following settings: –no-mixed –no-discordant –gbar 1000 –end-to-end. transcript abundance […]

2017
PMCID: 5436647
PMID: 28545050
DOI: 10.1371/journal.pone.0176522

[…] resulting fastq files were collected and demultiplexed to each barcode for post run data analysis., the sequenced reads were first chastity filtered then assessed for quality with fastqc [21]. ea-utils, version 1.1.2–537 [22], was then used to filter out low quality reads and trim out illumina adaptor sequences. reads were aligned to the h37rv genome (genbank nc_000962) using […]

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