Search Results for "forge genome assembler"
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Showing 28 open source projects for "forge genome assembler"
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genome-wb3-asm
A Genetic Algorithm Library written in Amiga Workbench 3.x assembler
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HipMer
A High performance distributed memory assembler for big genomic data
HipMer is the first end-to-end de novo genome assembler designed for extreme scale analysis via efficient parallelization. The single-genome assembly implementation is a high-performance parallelization and port of the Meraculous assembler (http://jgi.doe.gov/data-and-tools/meraculous/). The MetaHipMer extension is a recent addition to HipMer that is geared to large metagenomes and leverages iterative kmer sizes and a specialized scaffolding algorithm to produce increased contiguity and accuracy in metagenomic assemblies. ... -
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dnaasm
set of tools for NGS data analysis
genome de novo assembler for next generation sequencing data, tool to link contigs by long DNA reads -
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Phusion2
The genome assembly pipeline based on read clustering
...Setting a minimum threshold of shared k-tuples, the whole set of reads can then be clustered into groups using kmer sharing information in the relational matrix. After obtaining small read clusters with a controllable size, a local assembler can be used to produce contigs. -
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MIRA V5 is available only on GitHub! The V4 version released here on SourceForge stay up as some automated release fetching packages rely on V4. MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
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Meraculous-2D
Eukaryotic Genome Assembler
---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Efficient k-mer counting and deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. ... -
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GAVGA
A Genetic Algorithm for Viral Genome Assembly
GAVGA is a Genetic Algorithm for Viral Genome Assembly. It can be used in the assembly of small genomes, like viral ones. -
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metasort
A metagenome assembler by reducing microbial community
Most current approaches analyze metagenomic data with the participation of reference genomes. However, novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities still remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on... -
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Meta Assembler for de novo assembly results. GARM (Genome Assembly Reconciliation and Merging) is a pipeline to merge results from different assemblers or results from different DNA sequencing technologies.
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MaxInfo
Transcriptome assembler for RNA-seq
MaxInfo is an automated transcript discovery and quantification software designing for high-throughput RNA sequencing (RNA-seq). Assembling transcripts from reads are challenging because of the unpredictable uncertainties arising from completing full genome structure with very partial observations. MaxInfo tackles this problem by explicitly reducing the inherent uncertainties in the biological system caused by missing information. -
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RECORD
Assisted Genome Assembler
Assisted Genome Assembler -
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Opera
An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads. An updated version called OPERA-LG has been re-engineered with features for the assembly of large and complex genomes. -
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GFinisher
genome assembler finisher, gap, gap close, sort contig
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. contact dievalg at gmail.com -
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SWAP-Assembler
A scalable and fully parallelized genome assembler
There is a growing gap between the output of new generation massively parallel sequencing machines and the ability to process and analyze the sequencing data. We present SWAP-Assembler, a scalable and fully parallelized genome assembler designed for massive sequencing data. Intend of using traditional de Bruijn Graph, SWAP-Assembler adopts multi-step bi-directed graph (MSG). With MSG, the standard genome assembly (SGA) is equivalent to the edge merging operations in a semi-group. Then a computation model, SWAP, is designed to parallelize semi-group computation. ... -
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Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.
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BASE
a fast and accurate de novo genome assembler for longer NGS reads
BASE is developed for assembly of longer NGS data especially for HiSeq and MiSeq data. Deeply sequenced small genomes and large genome are all could be assembled well. You can also find the files in github: https://github.com/dhlbh/BASE -
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DNA Scissor is new software which provides users with a set of easy-to-use tools to perform several operations mainly: quality trimming, vector masking, vector-like contaminants removal, and repeats identification.
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miRLAB
miRLAB: an R package for exploring miRNA-mRNA regulatory relationships
...The package provides a complete set of pipelines for testing new methods and analysing new expression datasets. miRLAB includes a pipeline to obtain matched miRNA and mRNA expression datasets directly from The Cancer Genome Atlas (TCGA, based on TCGA Assembler), the benchmark computational methods for inferring miRNA-mRNA regulatory relationships, the functions for validating the predictions using miRNA experimentally validated target data and miRNA transfection data, and tools to compare the results from different computational methods. -
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SOAPdenovo2
Large-size genome de-novo assembler
What's next of SOAPdenovo2: MEGAHIT is the formal successor of SOAPdenovo2 MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph http://www.ncbi.nlm.nih.gov/pubmed/25609793 https://github.com/voutcn/megahit Latest Code on GitHub: https://github.com/aquaskyline/SOAPdenovo2 SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed... -
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Hybrid De Novo Assembler (HyDA)
Genome co-assembler particularly for single-cell short read data
Refer to http://chitsazlab.org/software/hyda/ and http://chitsazlab.org/software/squeezambler for citations of HyDA and Squeezambler. -
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Suffix Grove
Suffix Grove: Genome Sequence Assembly by Suffix Tree Branch Extension
Suffix Grove is a genome sequence assembler that employs a novel algorithm based on suffix trees. It is designed to demonstrate the utility of the algorithm and is not suited to full-scale assembly efforts. -
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Cerulean Hybrid Genome Assembler v0.1 Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. I am not able to maintain and update the software due to change in research funding. However I will be happy to answer any queries or provide support and comments if you are interested in extending this algorithm.
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PASHA: Parallelized Short Read Assembly
One of the fastest parallel short read assemblers for large genomes.
PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. ... -
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PRICE de novo (meta)genome assembler
Targeted de novo assembly of (meta)genomic components
PRICE (Paired-Read Iterative Contig Extension) is a command-line de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, those contigs can be individual reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non-paired data, or contigs that were output from a prior run of PRICE or any other assembler. ...