Base calling software tools | High-throughput sequencing data analysis
Next-generation sequencing platforms are dramatically reducing the cost of DNA sequencing. With these technologies, bases are inferred from light intensity signals, a process commonly referred to as base-calling. Thus, understanding and improving the quality of sequence data generated using these approaches are of high interest.
Manages base call (BCL) conversion to FASTQ and demultiplexing. BCL2FASTQ’s sample demultiplexer allows users to: generate statistics, regenerate analysis plots for each multiplexed sample, copy raw matrix, phase file and update sample sheet. Furthermore, this program includes features to mask multiple adapter sequences per read with a configurable stringency of the adapter and has standard Illumina adapter sequences.
Provides various next-generation sequencing (NGS) data analysis applications which are developed or optimized by Illumina, or from a growing ecosystem of third-party app providers. BAseSpace is a cloud platform that can be integrated with the industry’s leading sequencing platforms, without cumbersome or time consuming data transfer steps.
Allows users to generate cluster generation and sequencing for Illumina data. HSC is able to create base calls and quality metrics in real time by reducing the whole-genome data storage footprint. HSC offers an integrated focus feature to ensure reliable image capture and real time analysis (RTA) and provides fast access to quality metrics. The interface provides run configuration screen that contains dropdown lists, checkboxes or text fields to enter information for your run.
Provides various apps and services run on the EPI2ME operating system which will support the analysis of any living thing, by any user and in any environment. The Metrichor platform is available to users of Oxford Nanopore's MinION - and soon the PromethION. MinION is currently used for the analysis of nucleic acids. Applications made available by Metrichor enable analysis of the resulting experimental data, for example identifying species in a sample by analysing DNA.
Assists in reducing the error rate and increasing the output of usable reads. Ibis is a base caller for the Illumina sequencing system that provides sequences with a lower number of base calling errors and better quality-scores with each base. It facilitates quality filtering of the data, sequence read mapping, de novo assembly and data analysis like single nucleotide polymorphism (SNP) calling.
Enables base-calling for high-throughput sequencing. naiveBayesCall is a base-calling algorithm based on the same graphical model as in BayesCall. The software utilizes approximation and optimization methods to achieve scalability. It is able to estimate local parameters using a small number of clusters. naiveBayesCall was tested using using a standard resequencing data of PhiX174 virus, obtained from Illumina’s Genome Analyzer platform.
Assists users with pyrosequencing reads. PyroBayes is a base calling program that enables single-nucleotide polymorphism (SNP) calling in resequencing applications, including in shallow read coverage. It was developed for the 454 Life Sciences sequencing machines. This application aims to determine the most likely number of incorporated bases from the measured incorporation signal for each nucleotide test.