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See the kallisto | bustools website for examplesĪnd instructions on how to use bustools as part of a single-cell RNA-seq workflow.īurrows-Wheeler Aligner (BWA) is an efficient program that aligns It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibilityĬount matrices, and is useful for many other tasks. Greater similarity of length 25 bases or more.īLIS is a portable software framework for instantiating high-performanceīLAS-like dense linear algebra libraries.īustools is a program for manipulating BUS files for single cell RNA-Seq datasets. Sequences of different proteins or the nucleotides of DNA sequences.īLAT on DNA is designed to quickly find sequences of 95% and and Marchini, J., “BGEN: a binary file format for imputed genotype and haplotype data”,īasic Local Alignment Search Tool, or BLAST, is an algorithmįor comparing primary biological sequence information, such as the amino-acid The library can be used as theīasis for BGEN support in other software, or as a reference forĭevelopers writing their own implementations of the BGEN format.īand, G. This repository contains a reference implementation ![]() The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and Tasks can be easily split by chromosome forĭistributing whole-genome analyses across a computational cluster.īEDTools: a powerful toolset for genome arithmetic. Other management of genomic data of arbitrary scale. Scalable Boolean and other set operations, statistical calculations, archiving, conversion and Samtools is a suite of programs for interacting with high-throughput sequencing data.īEDOPS is an open-source command-line toolkit that performs highly efficient and This bundle collect the standard GNU build tools: Autoconf, AutomakeīAli-Phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid,īBMap short read aligner, and other bioinformatic tools. MP3 TOOLKIT 1.0.5 PORTABLE GENERATORTemplate file that lists the operating system features that the package canĪutomake: GNU Standards-compliant Makefile generator Autoconf creates a configuration script for a package from a MP3 TOOLKIT 1.0.5 PORTABLE MANUALThese scripts canĪdapt the packages to many kinds of UNIX-like systems without manual user To automatically configure software source code packages. ![]() PyArrow Python bindings), a cross-language development platformĬonnect is an install-on-demand Web browser plug-in that facilitates high-speed uploads andĭownloads with an Aspera transfer server.Īutoconf is an extensible package of M4 macros that produce shell scripts ![]() Sensitivity were important design criteria.Īpache Arrow (incl. It was developed for the use in a clinical research setting. MP3 TOOLKIT 1.0.5 PORTABLE ARCHIVEProvide an interface to ZIP archive files.ĪrrayFire is a library of accelerated tensor computing functions.Īrriba is a command-line tool for the detection of gene fusions from RNA-Seq data. That empowers companies to adopt a modern open data science analytics architecture.Īpptainer is a portable application stack packaging and runtime utility. The Anaconda platform provides an enterprise-ready data analytics platform Using the ATK interfaces, accessibility tools haveįull access to view and control running applications.ĪUGUSTUS is a program that predicts genes in eukaryotic genomic sequencesĪdapterRemoval searches for and removes remnant adapter sequencesįrom High-Throughput Sequencing (HTS) data and (optionally) trims low quality basesįrom the 3’ end of reads following adapter removal.ĪlphaFold can predict protein structures with atomic accuracy even where no similar structure is knownīuilt to complement the rich, open source Python community, ASE uses it automatically when installed.ĪTK provides the set of accessibility interfaces that are implemented by other A parallel, multi-engine simulator for heterogeneous swarm roboticsĪSE is a python package providing an open source Atomic Simulation Environmentįrom version 3.20.1 we also include the ase-ext package, it contains optional reimplementations ![]()
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