Search Results for "bowtie2-2.5.2"
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Showing 18 open source projects for "bowtie2-2.5.2"
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HubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
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For minor company expenses, you might utilize a spend management solution or track everything in spreadsheets. For everything more, you'll need Precoro. We help companies achieve procurement excellence and budget efficiency by building transparent, predictable, automated spending workflows.
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Tria Sistema Operatiu
Helps you find, download & burn the best Operating System for any PC
Tria Operating System detects hard & soft specs of the PC where you run the program, offering the ability to load this info or specify it manually to let the program inform you what would be the best operating system for a specific PC, with the specified hardware, and then see the difference by adding RAM, a SSD hard drive, changing the graphics card ... etc. REQUIREMENTS: For Linux, you need GAMBAS 3.3 or later, so you will have to install the gambas3 package before installing. 90's... -
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koa-verto
Middleware for Koa that adds version header (x-version) to response
Middleware that adds headers X-Service-Name & X-Service-Version to the response of Koa. Inspired by koa-version-header. -
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TARGT pipeline
Targeted Analysis of sequence Reads for GenoTyping of HLA/MHC genes
.... The pipeline also requires installed versions of the mapping tool Bowtie2 and samtools. -
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PPLine
SNP calling, annotation and gene/transcripts expression quantification
PPLine is a Python-based suite aimed to process raw RNA-seq or Exome-seq data. PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration of the results -
Evolia is a web and mobile platform that connects enterprises with 1000’s of local shift workers and offers free workforce scheduling and time and attendance solutions. Is your business on Evolia?
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CNVMM
CNVMM performs copy number variations detection
CNVMM specializes in identifying copy number variations (CNVs) when there are repeated sequences in the reference genome. The input file is a single short read mapping result from any short read aligners. However, NNmapper or Bowtie2, which detect all mapping results for multi-reads, are recommended. To use the code, MATLAB installation is required. Mac or Linus system is required. -
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Identifies rRNA, contaminants, trims in a standard fashion etc. Maintains read pairs. Built for fire-and-forget high throughput projects (terabytes of data). Uses pbzip2, bowtie2, fastx_toolkit, samtools, fastqc, Trimmomatic (optional)
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Faligner
Faligner: a Local Sequence Alignment Ubuntu Package
A package based on 3 local alignment tools i.e., Bowtie, Bowtie2 and BWA. Package covers single-end, paired-end alignments. Moreover, the package also demonstrates overlap alignment and colorspace alignment features. The package also includes graphical user interface to make it interactive. -
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MutAid
MutAid: Sanger and NGS based pipeline for mutation screening.
..., variant calling, variant annotation and co-analyze Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as deletions and insertions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms (Sanger, Illumina, 454 and Ion Torrent) and five read mappers including BWA,TMAP, Bowtie,Bowtie2 and GSNAP and four variant callers -
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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. -
It protects your internal resources such as behind-the-firewall applications, teams, and devices.
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CUSHAW3 is an open-source parallelized, sensitive and accurate short-read aligner. This aligner proposes a general approach to properly aligning both easy and hard reads to large genomes such as the human genome. Perform evaluation on alignment quality reals that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novalign3 for short-reads...
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SOAP3-DP
Fast, Accurate and Sensitive GPU-based Short Read Aligner
Latest Code on GitHub: https://github.com/aquaskyline/SOAP3-dp SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads... -
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openSEQ
NGS compute distro proloaded with pipeline analysis software
... tab links to our pipeline constructer. The second homepage tab links to a xterm session on the client. Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk -
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AFSM_seq
a simple and rapid method for genome-wide SNP and methylation site
... aligned to the reference genome using the Bowtie2, allowing a maximum of four mismatches and one gap of up to 3 bp. Using the SAMtools pileup command the variable positions (SNPs) were determined. 5.AFSM_meth_V_1.0.pl are used for analyses of AFSM methylation results were based on comparisons of assembled sequences . perl AFSM_meth_V_1.0.pl -i output.sort.bam -o output.meth.matrix -
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dna-bison
Bisulfite alignment On Nodes of a cluster
Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2. Multiple compute nodes are not absolutely required, but will make the alignment process faster. Further details available on the Wiki page. Help also available on SEQanswers (http://seqanswers.com/forums/showthread.php?t=31314) or by creating a ticket here. You can now track the development... -
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Software quality assurance is essential in genomic medicine. Nonetheless there is currently no systematic evaluation of existing computational tools used for whole genome or whole exome sequencing data analysis. We developed a Metamorphic Testing tool that tests three widely used short-read alignment programs (BWA, Bowtie and Bowtie2) in order to systematically evaluate their performance.
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CPS StopWatch
A little stopwatch to manage your time
... Santos) + 2.5.2 - Layout fix on report window (Tiago_Farias) - Auto PIN and double click on PIN button FIX (Fabiano_Ferreira) + 2.5 - Added Configuration Possibility - Added button to Configuration on Main Screen - Added Information Button on Main Screen - Improved time algorithm - Utilization of a Config.ini file to save personalizated settings. + 2.4.1 - Removed minimize button from main window - Fixed sound on last 20 seconds when using Windo -
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srst
Short Read Sequence Typing
Update - SRST2 Now Available ------ 25 Sep, 2013 This project has now been replaced by SRST2 - Short Read Sequence Typing for Bacterial Pathogens, available at http://katholt.github.io/srst2/ The new SRST2 program does gene typing as well as MLST (e.g. typing resistance genes, virulence genes, etc). SRST2 is faster and more accurate than the old SRST, using bowtie2 to achieve local alignments (no need for flanking sequences) and a brand new scoring system. -
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Nexuiz is a multiplayer first-person shooter. It is distributed under the GNU General Public License (GPLv2). Version 1.0 was released on May 31, 2005. The current version is, 2.5.2.
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