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Zarr — zarr 2.1.5.dev40+dirty documentation

Zarr is a Python package providing an implementation of chunked, compressed, N-dimensional arrays. Create N-dimensional arrays with any NumPy dtype. Chunk arrays along any dimension. Compress chunks using the fast Blosc. Meta-compressor or alternatively using zlib, BZ2 or LZMA. Store arrays in memory, on disk, inside a Zip file, on S3, . Read an array concurrently from multiple threads or processes. Write to an array concurrently from multiple threads or processes. Install Zarr from PyPI:. Git clone - re...

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Zarr — zarr 2.1.5.dev40+dirty documentation | zarr.readthedocs.io Reviews

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Zarr is a Python package providing an implementation of chunked, compressed, N-dimensional arrays. Create N-dimensional arrays with any NumPy dtype. Chunk arrays along any dimension. Compress chunks using the fast Blosc. Meta-compressor or alternatively using zlib, BZ2 or LZMA. Store arrays in memory, on disk, inside a Zip file, on S3, . Read an array concurrently from multiple threads or processes. Write to an array concurrently from multiple threads or processes. Install Zarr from PyPI:. Git clone - re...

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Zarr — zarr 2.1.5.dev40+dirty documentation | zarr.readthedocs.io Reviews

https://zarr.readthedocs.io

Zarr is a Python package providing an implementation of chunked, compressed, N-dimensional arrays. Create N-dimensional arrays with any NumPy dtype. Chunk arrays along any dimension. Compress chunks using the fast Blosc. Meta-compressor or alternatively using zlib, BZ2 or LZMA. Store arrays in memory, on disk, inside a Zip file, on S3, . Read an array concurrently from multiple threads or processes. Write to an array concurrently from multiple threads or processes. Install Zarr from PyPI:. Git clone - re...

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alimanfoo.github.io

Estimating F

http://alimanfoo.github.io/2015/09/21/estimating-fst.html

Sep 21, 2015. In phase 1 of the Ag1000G project. We have whole genome sequence data for mosquitoes from 9 African countries. As part of our analysis of population structure, I recently needed to calculate average F. Between each pair of populations. I also needed to calculate F. In windows over the genome, to look for genome regions that are particularly differentiated between certain populations. Pointed me to Bhatia et al. (2013). Which provides some clear advice on how to estimate F. SortedIndex shape...

alimanfoo.github.io

Genotype compressor benchmark

http://alimanfoo.github.io/2016/09/21/genotype-compression-benchmark.html

Sep 21, 2016. This blog post benchmarks different compressors for use with genotype data from large-scale resequencing projects. TL;DR for speed you can’t beat Blosc LZ4, but Blosc Zstd Bitshuffle gives a very high compression ratio with good all-round performance. Why do I care about compression? Fast compression brings interactive analysis of genome variation data. The data used in this benchmark are genotype data from the Ag1000G project phase 1 AR3 data release. And can be downloaded via FTP. For the...

alimanfoo.github.io

A tour of scikit-allel

http://alimanfoo.github.io/2016/06/10/scikit-allel-tour.html

A tour of scikit-allel. Jun 10, 2016. This notebook contains a brief tour of some exploratory analyses that can be performed on large-scale genome variation data using scikit-allel. In combination with general purpose Python scientific libraries such as numpy. Project (phase 1) we have whole-genome sequence data from 765 individual mosquitoes collected from 8 different countries across Africa. We have used a standard approach. The goal of this tour is to give a flavour of:. How much coding is required.

alimanfoo.github.io

Fast PCA

http://alimanfoo.github.io/2015/09/28/fast-pca.html

Sep 28, 2015. Principal components analysis (PCA) is a mainstay of population genetics, providing a model-free method for exploring patterns of relatedness within a collection of individuals. PCA was introduced as a tool for genetic genetic analysis by Patterson, Price and Reich (2006). Subsequently Gil McVean (2009). Provide a concrete illustration of some of these issues, so I thought I’d try to bring together some experiences here. Includes a randomized SVD. Which provide a convenience layer between u...

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Zarr — zarr 2.1.5.dev40+dirty documentation

Zarr is a Python package providing an implementation of chunked, compressed, N-dimensional arrays. Create N-dimensional arrays with any NumPy dtype. Chunk arrays along any dimension. Compress chunks using the fast Blosc. Meta-compressor or alternatively using zlib, BZ2 or LZMA. Store arrays in memory, on disk, inside a Zip file, on S3, . Read an array concurrently from multiple threads or processes. Write to an array concurrently from multiple threads or processes. Install Zarr from PyPI:. Git clone - re...

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