Bam-readcount - rapid generation of basepair-resolution sequence metrics
نویسندگان
چکیده
Bam-readcount is a utility for generating low-level information about sequencing data at specific nucleotide positions. Originally designed to help filter genomic mutation calls, the metrics it outputs are useful as input variant detection tools and resolving ambiguity between callers . In addition, has found broad applicability in diverse fields including tumor evolution, single-cell genomics, climate change ecology, tracking community spread of SARS-CoV-2. Here we report on release version 1.0 this tool, which adds CRAM support, among other improvements. It released under permissive MIT license available https://github.com/genome/bam-readcount.
منابع مشابه
Precision surface-coupled optical-trapping assay with one-basepair resolution.
The most commonly used optical-trapping assays are coupled to surfaces, yet such assays lack atomic-scale ( approximately 0.1 nm) spatial resolution due to drift between the surface and trap. We used active stabilization techniques to minimize surface motion to 0.1 nm in three dimensions and decrease multiple types of trap laser noise (pointing, intensity, mode, and polarization). As a result, ...
متن کاملLearning Sequence Neighbourhood Metrics
Recurrent neural networks (RNNs) in combination with a pooling operator and the neighbourhood components analysis (NCA) objective function are able to detect the characterizing dynamics of sequences and embed them into a fixed-length vector space of arbitrary dimensionality. Subsequently, the resulting features are meaningful and can be used for visualization or nearest neighbour classification...
متن کاملSome Biological Sequence Metrics
Some new metria are introduced to measure the distance between biological sequences, such as amino acid sequences or nucleotide sequences. These metrics generalize a metric of Sellers, who considered only single deletions, mutations, and insertions. The present metria allow, for example, multiple deletions and insertions and single mutations. They also allow computation of the distance among mo...
متن کاملSome Biological Sequence Metrics*
Some new metrics are introduced to measure the distance between biological sequences, such as amino acid sequences or nucleotide sequences. These metrics generalize a metric of Sellers, who considered only single deletions, mutations, and insertions. The present metrics allow, for example, multiple deletions and insertions and single mutations. They also allow computation of the distance among ...
متن کاملEvaluation Metrics for Generation
Certain generation applications may profit from the use of stochastic methods. In developing stochastic methods, it is crucial to be able to quickly assess the relative merits of different approaches or models. In this paper, we present several types of intrinsic (system internal) metrics which we have used for baseline quantitative assessment. This quantitative assessment should then be augmen...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of open source software
سال: 2022
ISSN: ['2475-9066']
DOI: https://doi.org/10.21105/joss.03722