qaTools protocols

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qaTools specifications

Information


Unique identifier OMICS_27493
Name qaTools
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format BAM,SAM
Operating system Unix/Linux
Programming languages C, C++
Computer skills Advanced
Stability Stable
Maintained Yes

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qaTools in pipeline

2017
PMCID: 5740502
PMID: 29242367
DOI: 10.15252/msb.20177589

[…] reads were mapped at 97% identity and multiple mappers were discarded. computation of genome coverage for each speci cluster was performed using qacompute (https://github.com/costeapaul/qatools), resulting in estimations of both horizontal and vertical coverage per sample, per genome., population snps were called using metasnv (costea et al, ), which resulted in 19,221,237 positions […]


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qaTools in publications

 (5)
PMCID: 5740502
PMID: 29242367
DOI: 10.15252/msb.20177589

[…] reads were mapped at 97% identity and multiple mappers were discarded. computation of genome coverage for each speci cluster was performed using qacompute (https://github.com/costeapaul/qatools), resulting in estimations of both horizontal and vertical coverage per sample, per genome., population snps were called using metasnv (costea et al, ), which resulted in 19,221,237 positions […]

PMCID: 5701178
PMID: 29176730
DOI: 10.1038/s41598-017-16353-x

[…] counted only when they were mapped with greater than 97% identity. we computed horizontal and vertical coverage per sample over each of the genomes using qacompute (https://github.com/costeapaul/qatools)., the alignment results were imported into megan 5 and taxa assignments were done with strict parameters of the lca-assignment algorithm and considering the read length generated […]

PMCID: 5349250
PMID: 28291265
DOI: 10.1038/sdata.2017.32

[…] was able to perform the cortical surface reconstruction fully automatically and without any errors during processing. afterwards freesurfer’s qa tools v1.1 (https://surfer.nmr.mgh.harvard.edu/fswiki/qatools) have been used and no outliers were identified. visual inspection shows good surface reconstructions, but manual intervention could improve results of all datasets. however, this is beyond […]

PMCID: 4556927
PMID: 26346238
DOI: 10.1038/sdata.2015.44

[…] each folder has four sub-folders, namely t1qa, restqa1, restqa2, and dtiqa, for modality-specific qa analysis results. the t1qa folder contains t1 qa analysis results using the freesurfer qa tools (qatools_v1.1.tar, https://surfer.nmr.mgh.harvard.edu/fswiki/qatools), which are mainly screenshots of various volumes/surfaces resulting from the recon-all pipeline. the restqa1 folder is composed […]

PMCID: 4493802
PMID: 26149490
DOI: 10.1186/s12888-015-0546-2

[…] from both fes patients and hcs were extracted. all results of cortical parcellations were examined by both visual inspection and freesurfer qa tools (available from http://www.freesurfer.net/fswiki/qatools)., statistical analysis was performed with statistical package for social sciences, version 17.0 (spss inc., chicago, illinois). differences in age and educational levels among the three […]


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