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Fastaq specifications


Unique identifier OMICS_19987
Name Fastaq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ, GFF3, EMBL, GBK, Phylip
Output format GZIP
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.15.0
Stability Stable
Source code URL
Maintained Yes




No version available

Fastaq citations


Small RNAs of Haloferax mediterranei: Identification and Potential Involvement in Nitrogen Metabolism

PMCID: 5852579
PMID: 29439418
DOI: 10.3390/genes9020083

[…] dependence in count data was estimated and tested for differential expression; this was based on a model using the negative binomial distribution between nitrate and ammonium group samples.Both raw (FASTAQ files) and processed data (normalised counts) are available on the Gene Expression Omnibus (GEO) database (Series entry number: GSE108616) [].Mfold was used to predict the secondary structure o […]


Dissection of affinity captured LINE 1 macromolecular complexes

PMCID: 5821459
PMID: 29309035
DOI: 10.7554/eLife.30094.037
call_split See protocol

[…] e created by combining the human genome and ORFeus-Hs from pLD401 (); : ORFeus-Hs_pLD401.gbk). To map sequencing reads onto the reference genome and produce differential gene expression analysis: (1) FASTAQ files were trimmed via trimmomatic () using the following parameters: -phred33 -threads 8, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:16 MINLEN:25; (2) mapping was performed via STAR () version 2.5.3 […]


Whole genome sequencing of Oryza sativa L. cv. Seeragasamba identifies a new fragrance allele in rice

PLoS One
PMCID: 5708779
PMID: 29190814
DOI: 10.1371/journal.pone.0188920

[…] ations in BADH2 gene and its promoter. Data from this study was submitted to NCBI under BioProject ID PRJNA324355 and BioSample ID SAMN05200854. Raw reads of this project were deposited in compressed FASTAQ format at SRA database of NCBI with the accession number SRP076132 ( genome sequencing of the genomic DNA from Seeragasamba produced 42.6 x 106 r […]


Comparative Metagenomic Analysis of Electrogenic Microbial Communities in Differentially Inoculated Swine Wastewater Fed Microbial Fuel Cells

PMCID: 5660801
PMID: 29158944
DOI: 10.1155/2017/7616359

[…] s constructed for shotgun sequencing and a 150 paired-end sequencing reaction was performed on MiSeq platform (Illumina, San-Diego, CA, USA).The sequencing data were uploaded to the MG-RAST server as FASTAQ files for processing, primary analysis, and storage. Sus scrofa (pig) genome sequences were marked for exclusion during data submission. Primary submission data and results of the MG-RAST pipel […]


Comparison of classical multi locus sequence typing software for next generation sequencing data

Microb Genom
PMCID: 5610716
PMID: 29026660
DOI: 10.1099/mgen.0.000124

[…] coverage over the MLST genes was assessed by artificially generating perfect paired-ended reads with a length of 125 bases and a median insert size of 400 bases with varying levels of coverage using fastaq (v3.14.0). The allele sequences plus 500 base flanking regions were extracted from S. enterica Typhi CT18 [], accession number AL513382, and artificial paired-end reads were generated with mean […]


Viral genetic variation accounts for a third of variability in HIV 1 set point viral load in Europe

PLoS Biol
PMCID: 5467800
PMID: 28604782
DOI: 10.1371/journal.pbio.2001855
call_split See protocol

[…] biguous base as defined by the International Union of Pure and Applied Chemistry (IUPAC) notation was called when the most frequent base was in less than 60% of reads. The programs Trimmomatic [] and Fastaq [] were used to trim adapters, PCR primers, and low-quality bases from the reads; BLASTN [] was used to identify contigs and reads suspected of being contaminants; MAFFT [] was used to align th […]


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