XSQ Tools specifications

Information


Unique identifier OMICS_19770
Name XSQ Tools
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format XSQ, CSFASTA+QUAL
Output format XSQ, CSFASTA+QUAL, FASTQ
Operating system Unix/Linux
Computer skills Advanced
Version 20120109
Stability Stable
Maintained No

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XSQ Tools in publications

 (5)
PMCID: 4969619
PMID: 27481162
DOI: 10.1038/srep30980

[…] the cdna library was sequenced on an abi solid 5500 sequencer (life technologies) using paired-end 75 + 35 bp runs. for analysis, raw sequencing data was converted to csfastq using solid’s xsq_tools and local perl scripts. cleaning filters were applied to data files, based on fastqc quality control statistics, and solid sequencing adaptors detected with cutadapt. reads were clipped […]

PMCID: 4728584
PMID: 26797630
DOI: 10.3390/v8010025

[…] solid total rnaseq kit (applied biosystems). libraries were sequenced on the solid 4 platform., the raw csfasta and qual files produced by each run of solid 4 were converted to xsq files using the xsq tools package from life technologies™ (thermo fisher scientific). reads within these xsq files were mapped to the crpv genome using “genomic resequencing” mapping within lifescope™ from life […]

PMCID: 4617633
PMID: 26468746
DOI: 10.1016/j.chom.2015.09.009

[…] plaque being assigned to a unique pair of libraries. sequencing was performed in a solid 5500 xl machine (life technologies)., raw sequence data were converted to fastq format using the solid system xsq tools, 5′ end adapters and pcr primers were removed using cutadapt 1.6, sequences were trimmed to 75 bases using fastxtookit v0.014, and prinseq v0.20.4 was used for de-replication (removal […]

PMCID: 4412624
PMID: 25919614
DOI: 10.1371/journal.pone.0126289

[…] together after tag modification. the processing of the solid mate-paired data is more involved. solid mate-paired data are provided in a xsq file [], which is decomposed into two pairs of files by xsq tools (ver. 1.5) []. each pair consists of a short read file and a quality file. the short read data are then down-sampled referring to the quality values [] as follows. for each short read, […]

PMCID: 3912139
PMID: 24498386
DOI: 10.1371/journal.pone.0087875

[…] sequencer 5500xl solid system (life technologies) according to the manufacturer's instructions. xsq files generated from the 5500xl solid sequencer were converted into csfasta and qual files using xsq tools. then, sequenced reads were aligned to the national center for biotechnology information (ncbi) refseq reference sequence and sage tags were counted using solid sage analysis software v1.10 […]


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