NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.
In many next-generation sequencing (NGS) studies, a number of samples or data varieties are profiled for every particular person. An necessary high quality management (QC) step in these studies is to make sure that datasets from the identical topic are correctly paired.
Given the heterogeneity of data varieties, file varieties and sequencing depths in a multi-dimensional research, a sturdy program that gives a standardized metric for genotype comparisons can be helpful.
Here, we describe NGSCheckMate, a user-friendly software bundle for verifying sample identities from FASTQ, BAM or VCF information. This device makes use of a model-based technique to check allele learn fractions at recognized single-nucleotide polymorphisms, contemplating depth-dependent habits of similarity metrics for an identical and unrelated samples.
Our analysis reveals that NGSCheckMate is efficient for quite a lot of data varieties, together with exome sequencing, whole-genome sequencing, RNA-seq, ChIP-seq, focused sequencing and single-cell whole-genome sequencing, with a minimal requirement for sequencing depth >>0.5X).
An alignment-free module could be run immediately on FASTQ information for a fast preliminary examine. We advocate utilizing this software as a QC step in NGS studies.BACKGROUND
An built-in software for virus group sequencing data evaluation.
A virus group is the spectrum of viral strains populating an contaminated host, which performs a key function in pathogenesis and remedy response in viral infectious illnesses. However computerized and devoted pipeline for deciphering virus group sequencing data has not been developed but.
We developed Quasispecies Analysis Package (QAP), an built-in software platform to handle the issues related to making organic interpretations from huge viral inhabitants sequencing data. QAP gives quantitative perception into virus ecology by first introducing the definition “virus OTU” and helps a variety of viral group analyses and outcomes visualizations.
Various types of QAP have been developed in consideration of broader customers, together with a command line, a graphical person interface and an online server.
Utilities of QAP have been totally evaluated with high-throughput sequencing data from hepatitis B virus, hepatitis C virus, influenza virus and human immunodeficiency virus, and the outcomes confirmed extremely correct viral quasispecies traits associated to organic phenotypes.
QAP gives a whole answer for virus group excessive throughput sequencing data evaluation, and it will facilitate the straightforward evaluation of virus quasispecies in medical purposes.