base calling and alignment

USAGE SUMMARY

The phrase "base calling and alignment" is correct and usable in written English.
It is typically used in the context of bioinformatics or genomics, referring to the processes of determining the sequence of bases in DNA and aligning sequences for comparison. Example: "After the sequencing process, we proceeded with base calling and alignment to analyze the genetic variations."

✓ Grammatically correct

Science

Human-verified examples from authoritative sources

Exact Expressions

10 human-written examples

The Genome Analyzer Pipeline Software (Pipeline) was used to perform the early data analysis of the sequencing run, including the image analysis, base calling, and alignment.

Plosone

Base calling and alignment to the reference genome were performed using Torrent Suite 3.6 (Life Technologies).

EMBO Molecular Medicine

This provides an improved basis for analysis and algorithm design, e.g. for base calling and alignment.

Bioinformatics

Visual inspection and correction of base calling and alignment were performed at this stage.

BMC Evolutionary Biology

PyroBayes (v1.1) and Mosaik (v0.9.0891) algorithms were used in sequence base calling and alignment.

Annals of Neurology

Base calling and alignment were performed using the algorithm of PyroBayes and Mosaik.

Human Molecular Genetics

Human-verified similar examples from authoritative sources

Similar Expressions

50 human-written examples

The basic model, JointSNVMix1, assumes the data have perfect base calls and alignment, whereas the extended model, JointSNVMix2 (JSM2), weighs each read by base and mapping quality.

Bioinformatics

The images were analyzed with the pipeline software (version 1.0, Illumina software) to undertake base calling and sequence alignment to the reference genome.

Plosone

Genotype calling is concerned with the endpoint following base calling and sequence alignment.

Bioinformatics

Errors in base calling and read alignment present additional challenges for achieving sensitive and specific somatic variant calls.

BMC Genomics

There were artifacts caused by systematic errors in sequencing, base calling, and read alignment that the probabilistic model could not remove.

Cell Research

Expert writing Tips

Best practice

When describing a sequencing workflow, clearly delineate the specific software and algorithms used for both base calling and alignment to ensure reproducibility and clarity in your methods.

Common error

Avoid using "base calling" and "alignment" interchangeably. Base calling is the process of assigning a nucleotide base to a signal, while alignment maps the sequenced reads to a reference genome. They are distinct but interdependent steps in sequence analysis.

Linguistic Context

The phrase "base calling and alignment" functions as a compound noun phrase, typically used as a subject or object within a sentence. Ludwig AI shows its presence mainly in the context of science.

Expression frequency: Uncommon

Frequent in

Science

100%

Less common in

News & Media

0%

Formal & Business

0%

Ludwig's WRAP-UP

The phrase "base calling and alignment" is a technical term from genomics, representing two crucial initial steps in processing DNA sequencing data. Grammatically correct and consistently used within scientific literature, its purpose is to describe specific methodologies and workflows. Ludwig examples confirm the phrase's prevalence in scientific contexts. Given its technical nature, the register is formal and scientific. Understanding this phrase is essential for anyone working with next-generation sequencing data, and Ludwig AI provides valuable context for its proper usage.

More alternative expressions

Phrases that express similar concepts, ordered by semantic similarity:

Raw data processing in genomics

Highlights the initial steps of raw data processing, including both base calling and alignment as foundational elements.

Sequence data pre-processing

Refers to the pre-processing steps applied to sequence data before further analysis, including the processes of base calling and alignment.

Bioinformatics analysis of sequencing data

Describes the overall analysis of sequencing data using bioinformatics tools, encompassing multiple steps including base calling and alignment.

Next-generation sequencing data processing

Broader term covering all processing steps for NGS data, including quality control, filtering, and analysis beyond just base calling and alignment.

Sequence read processing and mapping

Focuses on the action of processing and mapping sequence reads, rather than specifically calling bases and aligning them.

Mapping reads to a reference genome

Emphasizes the process of mapping sequence reads to a reference genome, a key part of the alignment stage but omitting the base calling aspect.

Read alignment and variant calling

Highlights the alignment of reads and subsequent identification of variants, shifting the focus from base calling to variant detection.

Genomic data analysis pipeline

Refers to the broader process of analyzing genomic data, which includes but isn't limited to base calling and alignment.

Sequence assembly and annotation

Focuses on assembling short sequences into longer contigs and annotating genomic features, rather than the initial steps of base calling and alignment.

De novo genome assembly

Describes assembling a genome without a reference, which is distinct from aligning to a reference after base calling.

FAQs

What is the role of "base calling and alignment" in genomic research?

In genomic research, "base calling and alignment" are crucial initial steps in analyzing sequencing data. Base calling converts raw signals from sequencing machines into nucleotide sequences, while alignment maps these sequences to a reference genome, enabling the identification of genetic variations and other genomic features.

How do "base calling and alignment" contribute to variant calling?

Accurate "base calling and alignment" are essential for reliable variant calling. Errors in either process can lead to false positives or negatives in variant detection, affecting the accuracy of downstream analyses.

What software tools are commonly used for "base calling and alignment"?

Commonly used software tools for "base calling and alignment" include Illumina's BaseSpace, BWA (Burrows-Wheeler Aligner), Bowtie, and specialized pipelines like the Genome Analysis Toolkit (GATK). The choice of tool depends on the sequencing platform, data volume, and specific analysis goals.

Why are quality scores important in the context of "base calling and alignment"?

Quality scores, such as Phred scores, provide a measure of confidence in the accuracy of base calls. Higher quality scores indicate a lower probability of error, and these scores are used to filter and refine alignments, improving the overall quality of genomic analyses. It's closely connected to "base quality and alignment".