Search Results for "genome assembly"
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Showing 89 open source projects for "genome assembly"
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering... -
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University, see http://arthropods.eugenes.org/EvidentialGene/ Construction refers to the combination of classical gene prediction, and more recent gene assembly (de-novo and genome-assisted) methods. The basic Evigene methods involve using available best-of-breed gene prediction... -
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FindPlasmids
Find plasmids in microbial genome assembly files
FindPlasmids identifies known plasmids in genome assembly files by using the assembly file to query a local Blast+ database of plasmid sequences. The FindPlasmids package includes executables for Mac OS X, Linux and Windows. Detailed instructions for making the local plasmid database, searching it, and identifying the plasmids are included in the FindPlasmids package. -
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GenTreat is a computational pipeline with an intuitive graphical interface, was developed for automated hybrid assembly of prokaryotic genomes, performs assembly using two assemblers, merges the results, and then orders and annotates the assembled genome. Validation using raw reads from 61 organisms demonstrated that is a viable alternative for automated hybrid assembly, eliminating the need for using extensive command lines.
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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... -
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Citrus
Citrus: Editing HiC data for de novo genome assembly
juicer and 3D-DNA are two tools that re-arranges HiC data (xxx.hic format) and splits/re-orders super-scaffold data (xxx.assembly) to improve de novo genome assembly. Juicebox was specifically designed to tune or adjust genomic sequences based on HiC data. However, the current Juicebox version does not have a function to save updated HiC data and to summarize chromosome sequences. Thus, we created Citrus which can edit super-scaffolds according to chromatin conformation data captured in xxx.hic... -
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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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lemonade_assemble
Specialized sequence assembly tools
Assorted tools for: 1. Assembly of pooled BACs from PacBIO reads. 2. Polymorphic genome assembly 3. Processing of Trinity transcriptomes 4. Modified versions of other people's code used in any of the above. 5. Fasta processing and miscellaneous programs and scripts. Documentation is rudimentary or nonexistant. -
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Phusion2
The genome assembly pipeline based on read clustering
Phusion2 is a pipeline for de novo genome assembly using NGS data. It is based upon a strategy called read clustering. Starting with kmer frequency analysis, this allows for a reasonable selection of the kmer sizes. K-tuples from raw reads are merged and sorted into a table so that multiple occurring kmer words shared by different reads can be linked. A relation matrix is used to record the shared kmer words among all the reads. Setting a minimum threshold of shared k-tuples, the whole set... -
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ImproveAssembly
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0206
The availability of biological information in public databases has increased exponentially. To ensure the accuracy of this information, researchers have adopted several methods and refinements to avoid the dissemination of incorrect information. However, manual curation ensures and enriches biological information. Additionally, the genomic finishing process is complex, resulting in increased deposition of drafts genomes. This introduces bias in other omics analyses because incomplete... -
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MitoZ: A toolkit for mitochondrial genome assembly, annotation and visualization. see https://github.com/linzhi2013/MitoZ
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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... -
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GATOOL - Genome Assembly Tool
The tool allows to perform a bacterial genome assembly.
GATOOL is a web interface whichs integrates several tools, with the purpose of to do a genome assembly task and provide to the users a nice and real experience. and a very fast way to genomes assembly. -
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Genome Downloader
Downloads genome data from NCBI based on search terms.
GenomeDownloader is a command-line Perl program to download genomic data (using wget) from NCBI. It has been recently (2017-10) completely rewritten to work with the "new" data organization structure at NCBI. Assembly completion level (i.e., Contig, Scaffold, Chromosome or Complete Genome) can also be selected as a criterion for downloading data. Genomic data can be downloaded from all organisms belonging to a certain taxon (e.g., Mammalia or 40674), and downloads can be limited to certain... -
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Genobuntu
Genobuntu Package for Next Generation Sequencing
Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software... -
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GMcloser
Closing the gaps in scaffolds with preassembled contigs
GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased... -
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BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.
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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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Basejumper is a viewer for genome assembly data. It is designed to read in assembled DNA sequences in ACE format from massively parallel (or “next-generation”) sequencing experiments (Illumina/Solexa and Roche/454).
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wgssat_nbfgr
WGSSAT: SSR Annotation Pipeline
WGSSAT provides a Graphical User Interface pipeline to mine and characterize SSR from Whole genome data. This pipeline integrates prediction of genes, ncRNA, repeats and SSR from whole genome assembly and mapping of these predicted SSR on to the genome (classified according to genes, ncRNA, repeats, exonic and intronic region) along with primer designing and mining of cross-species amplification markers. The mining of SSRs from whole genome provides valuable information on the abundance of SSRs... -
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QSdpR
Viral Quasispecies Reconstruction software based on QSdpR algorithm
This is a viral quasispecies reconstruction software for quasispecies assembly problem on mRNA viruses, which is based on a correlation clustering approach and uses semidefinite optimization framework. The software accepts a reference genome, a NGS read set aligned to this reference and set of SNP locations in the form of a vcf file and outputs an optimal set of reconstructed species genomes which describes the underlying viral population. -
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A project made by Khalid Bashir. It's simple linux program which evaultes the genome assembly with high speed and accuracy. Please read instuctions.md [Options] Argument 1 -> Name of the input fasta/fastaq file Argument 2 -> Sequence Limit (optional)(Default: 999999999) Argument 3 -> Usable scaffold length (optional)(Default: 2500) Argument 4 -> Number of Nucliotide to spit into contigs (optional)(Default: 25) Argument 5 -> Genome size (optional)
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metasort
A metagenome assembler by reducing microbial community
... on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations on simulated dataset, salivary and gut microbiomes, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. -
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PBSuite
Software for Long-Read Sequencing Data from PacBio
This currently hosts two projects created and maintained by Adam English. PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads. ----- PBJelly ----- Read The Paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768 PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high...