Search Results for "sam" - Page 3
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Showing 155 open source projects for "sam"
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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Host LLMs in Production With On-Demand GPUsDeploy your model, get an endpoint, pay only for compute time. No GPU provisioning or infrastructure management required.
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AnyThemeScreenSaver
Our Screen Saver for Windows allows You to see Images on any theme,
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endpoint-health
Standalone web application allowing to monitor end points availability
...This project is licensed under the WTFPL (Do What The Fuck You Want To Public License, Version 2) Copyright © 2017 spypunk spypunk@gmail.com This work is free. You can redistribute it and/or modify it under the terms of the Do What The Fuck You Want To Public License, Version 2, as published by Sam Hocevar. See the COPYING file for more details. -
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sfbf-ui
UI frontend for sfbf, a useful application to search for largest files
UI frontend for sfbf, a useful application to search for largest files on file systems It brings features such as : - Fast file search to locate largest files - Configurable search depth - Various export formats (txt, json, xml, html) - Regular expression matching This project is licensed under the WTFPL (Do What The Fuck You Want To Public License, Version 2) Copyright © 2017 spypunk spypunk@gmail.com This work is free. You can redistribute it and/or modify it under the terms of the Do What The Fuck You Want To Public License, Version 2, as published by Sam Hocevar. See the COPYING file for more details. -
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sfbf
Useful console application to search for largest files on file systems
...It brings features such as : - Fast file search to locate largest files - Configurable search depth - Various output formats (txt, json, xml, html, csv) - Regular expression matching This project is licensed under the WTFPL (Do What The Fuck You Want To Public License, Version 2) Copyright © 2017 spypunk spypunk@gmail.com This work is free. You can redistribute it and/or modify it under the terms of the Do What The Fuck You Want To Public License, Version 2, as published by Sam Hocevar. See the COPYING file for more details. -
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Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.
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jSAM is an Eclipse plugin integrating a set of tools for stochastic analysis of concurrent and distributed systems specified using process algebras. More specifically, jSAM provides tools that can be used for interactively executing specifications, for simulating their stochastic behaviour and for verifying property satisfaction via stochastic model-checking.
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Placnet
Placnet project
...It's been optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools. Please cite PLACNET as: Lanza VF, de Toro M, Garcillán-Barcia MP, Mora A, Blanco J, Coque TM, de la Cruz F: Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences. ... -
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
...Therefore, identification conserve and novel miRNA and their target genes in model and new sequenced species are inevitable. MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result). The program provide a step praramter (8 steps) which can allow running program from any step and finishing all remaining steps. You also can run step by step using each step program. Please run these step programs at the same directory for running main program MITP.pl. ... -
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CoverageAnalyzer
RNA modification detection by RT signatures in deep sequencing data
...Consequently, the community will profit from a platform seamlessly connecting detailed visual inspection of RT signatures and automated screening for modification candidates. CoverageAnalyzer was developed in response to the demand for a powerful inspection tool, running on all 3 OSes. With SAM standard as input and an intuitive GUI, even non-experts can accomplish a variety of tasks, from visualization of RNA Seq data, up to sophisticated modification analysis with significance-based candidate calling. -
Error to trace to log to deploy. One click. No SSH.AppSignal links every error to the trace, the trace to the log, the log to the deploy that shipped it.
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converts a SAM file to fasta file. SAM file is a file output from bwa alignment software. It outputs aligned fasta file.
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SeqPig
Use Apache Pig to process your large sequencing datasets!
...It provides import and export functions for file formats commonly used for sequencing data, as well as a collection of Pig user-defined-functions (UDF’s) to help process aligned and unaligned sequence data. Currently SeqPig supports BAM/SAM, FastQ and Qseq input and output. For more information see the manual at http://seqpig.sourceforge.net/ -
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Pathoscope
Predicts strains of genomes in Nextgen seq alignment file (sam/bl8)
This page is here for archival purpose. Please visit github for the latest version of the software: https://github.com/pathoscope PathoScope takes next-generation sequencing reads from a mixture sample and predicts which genomes are present. We use a Bayesian framework combined with an initial reference-based alignment to assign reads to the correct genome of origin. Pathoscope 2.0: Wiki: http://sourceforge.net/p/pathoscope/wiki/Home/... -
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A fork of BOSSA
This is a fork of the BOSSA project by ShumaTech.
BOSSA is a flash programming utility for Atmel's SAM family of flash-based ARM microcontrollers, developed by ShumaTech. The motivation behind BOSSA is to create a simple, easy-to-use, open source utility to replace Atmel's SAM-BA software. This project is a fork, created to temporarily host new modifications to BOSSA until they can be incorporated into the main BOSSA codebase. -
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RGAAT
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format). -
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Simple Automation Middleware (SAM) est un framework permettant de batir des applications sous forme de modules. Il fournit des bibliothèques COM Delphi implémentant la gestion des évènements, Dispatch etc...
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bio-cargo
CARGO - Compressed ARchival for GenOmics
CARGO is a high-level framework that can semi-automatically generate software systems optimized for the compressed storage of arbitrary types of large genomic data collections. Straightforward applications of CARGO methods to compress FASTQ and SAM format archives require only a few lines of code, produce solutions that match and sometimes outperform specialized format-tailored compressors, and scale well to multi-TB datasets. -
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sameflash
Serial flash tool for Atmel M7 core
This tool written in Java uploads HEX files into microcontroller flash and runs it using SAM-BA protocol, as original Atmel tool fails with modern M7 core chips. SAME70 is now supported. Current version does not program GPNVM bit, so after reset program will not start again - just add few lines of code to do that. -
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Sita Access Manager
Sita Access Manager (SAM) is php based Login System.
Sita Access Manager (SAM) is php based and secure login system. -
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samdrives
Monitor and control multiple SAM/QFS servers
samdrives is a tool for monitoring and controlling tape drives on multiple SAM/QFS servers simultaneously. It monitors performance (same as iostat), drive status (same as "samu t"), and allows controlling archiving, staging and tape drives remotely. -
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iMSAT represents a full update of the vcf2MSAT program. This command line python program allows for a user to use the polymorphism data generated using SAM- and BAM-tools and a .fasta alignment file to search for polymorphic microsatellite markers (MSATs or STRs). By identifying polymorphic makers, rather than simple repeat regions as previous programs have done, iMSAT greatly increases the speed at which polymorphic MSATs that can be identified -- saving researchers precious time and money. ...
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sam_comp
Compression for SAM/BAM file format
This is a simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format. -
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NUCPOS
Suite for analysis of genome-wide nucleosome positions
NUCPOS is a suite of utilities for the analysis of genome-wide nucleosome positions. The suite is currently composed of 5 programs: nucfrag dyad_bins align_dyads dinucleotide_frequencies hp_fft The analysis starts with the SAM format alignment file generated by an alignment program such as Bowtie2. All utilities are coded in C++ 11, and can easily be modified to use any available genome sequence. -
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SAMSVM
A tool for misalignment filtration on SAM-format sequences with SVM
Applying the LIBSVM, a package of support vector machine, SAMSVM was developed to correctly detect and filter the misaligned reads of SAM format. Such filtration can reduce false positives in alignment and the following variant analysis. -
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Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. ...
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SuRankCo
Supervised Ranking of Contigs in de novo Assemblies
...Renard (http://www.biomedcentral.com/1471-2105/16/240/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using SuRankCo. Update Jun2015: * Minor changes to enable BAM support. Update Feb2014: * Added support for FASTA/SAM assemblies in addition to ACE/FASTQ(QUAL). NOTE: features of FASTA/SAM assemblies do not include BaseCount, BaseSeqmentCount and ContigQualities yet.
