Displaying 1 to 11 from 11 results

BizTalk Factory

Library to speed up the development of BizTalk Server applications that shifts the focus from graphical editors to fluent C# code wherever possible.

BAM Service Generator

BizTalk BAM Service Generator is a command line to generate .NET 4.0 WCF services for BizTalk BAM activities.

sambamba - Tools for working with SAM/BAM/CRAM data

Sambamba is a high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Because of its efficiency is an important work horse running in many sequencing centres around the world today. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. Most tools support piping: just specify /dev/stdin or /dev/stdout as filenames. When we started writing sambamba (in 2012) the main advantage over samtools was parallelized BAM reading and writing. In March 2017 samtools 1.4 was released, reaching parity on this. A recent performance comparison shows that sambamba holds its ground and can do better in different configurations. Here are some comparison metrics. For example for flagstat sambamba is 1.4x faster than samtools. For index they are similar. For Markdup almost 6x faster and for view 4x faster. For sort sambamba has been beaten generally, though sambamba is up to 2x faster on large RAM machines.

viral-ngs - Viral genomics analysis pipelines

A set of scripts and tools for the analysis of viral NGS data. More detailed documentation can be found at http://viral-ngs.readthedocs.org/ This includes installation instructions, usage instructions for the command line tools, and usage of the pipeline infrastructure.

VerifyBamID - A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method

Motivation: Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis. Across many existing models, allele frequency usually is used to calculate prior genotype probability. Lack of accurate assignment of allele frequency could result in underestimation of contamination level. Hence we propose this ancestry-agnostic DNA contamination estimation method. Results: We applied our method to 1000 Genomes datasets by simulating contamination levels from 1% to 20% and comparing the contamination estimates obtain from different methods. When using pooled allele frequencies, as opposed to population-specific allele frequencies, we observed that the contamination levels are underestimated by 20%, 40%, 51%, and 73% for CEU, YRI, FIN, and CHS populations, respectively. Using our new method, the underestimation bias was reduced to 2-5%.

hts-nim-tools - useful command-line tools written to show-case hts-nim

This repository contains a number of tools created with hts-nim intended to serve as examples for using hts-nim as well as to be useful tools. each of these is described in more detail below.

dev-standards - https://bamtech.gitbooks.io/dev-standards/

⚠️ We are in process of migrating all the content to a private gitbook. The public content in this repository will be converted to blog articles for better acessibility. We are mobile developers, based in Paris, working with hybrid and cross platform technologies.

BioD - Bioinformatics library in D. (utils for working with SAM, BAM, SFF formats)

BioD is a fast and memory efficient bioinformatics library written in the D programming language. D is a language that suits parallel programming because of guarantees the compiler provides. D is both a low-level language and a high-level hybrid OOP/FP language. There is no other programming language that matches those features. Also, D templating/generics is far easier that that of C++ or, say, Scala.