Search Results for "genome"
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Showing 634 open source projects for "genome"
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genome-wb3-asm
A Genetic Algorithm Library written in Amiga Workbench 3.x assembler
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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BBMap
BBMap short read aligner, and other bioinformatic tools.
This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and... -
JobNimbus Construction SoftwareTrack leads, jobs, and tasks from one easy to use software. You can access your information wherever you are, get everyone on the same page, and grow your business.
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw... -
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A tool to estimate trends in recent effective population size trajectories using genome-wide SNP data.
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Lep-MAP3 is a novel and free software for linkage mapping. It can construct linkage maps on very large number of markers and individuals on single or multiple families. Especially, it supports whole genome sequencing data even with low sequencing depth. If you use Lep-MAP3, please cite P. Rastas. Lep-MAP3: Robust linkage mapping even for low-coverage whole genome sequencing data, Bioinformatics. 2017, 33(23):3726-3732. https://doi.org/10.1093/bioinformatics/btx494. Please note Lep-Anchor...
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crossmap
convert genome coordinates betweeen assemblies
CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies (eg. lift from GRCh36/hg18 to GRCh37/hg19 or vice versa).It support file in BAM, SAM, BED, Wiggle, BigWig, GFF, GTF format. -
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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... -
Qrvey allows SaaS companies to create richer products and bring them to market fasterQrvey is a low code embedded analytics platform built to help SaaS providers by simplifying the process of putting analytics tools in the hands of all users as fast as possible.
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GenoViz
Visualization software for genomics
GenoViz provides software applications and re-usable components for data visualization and data sharing in genomics. Our main products are * Integrated Genome Browser (IGB) * GenoViz SDK For more information about IGB, visit https://bioviz.org. Source code for IGB is available from https://bitbucket.org/lorainelab/integrated-genome-browser. For more information about GenoViz SDK, visit https://bitbucket.org/lorainelab/genoviz-sdk. Javadocs for GenoViz SDK are available at https... -
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popoolation
estimate natural variation and positive selection
PoPoolation is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation allows to calculate Tajima’s Pi, Watterson’s Theta and Tajima’s D with a sliding window approach for chromosomes or for set of genes. One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. We believe that PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. Documentation: https... -
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binocular
Binocular segmentation of whole-genome DNA sequence data
Segmentation-based detection of copy-number alterations and allelic imbalances in whole-genome DNA sequence data. -
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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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Lep-Anchor
Linkage map guided genome anchoring
Lep-Anchor has been developed to efficiently anchor genomes into chromosomes by using all the information provided by Lep-MAP3 and the additional information provided by long reads and contig-contig alignments to link contigs and to collapse haplotypes. Lep-Anchor supports millions of markers over multiple maps. Pasi Rastas, Lep-Anchor: Automated construction of linkage map anchored haploid genomes, Bioinformatics, btz978, https://doi.org/10.1093/bioinformatics/btz978 -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA 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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janda
structural variant detector
Janda is a tool to detect structural variants in whole-genome DNA sequence data. It identifies structural variants (deletions, duplications, translocations, and inversions) using anomalously mapped pair reads and realigning potential junction reads. -
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proSeq
ProSeq is a GUI program to edit and analyse DNA polymorphism datasets
... coalescent simulations and generate and visualise phylogenies. The main changes in Proseq4 compared to Proseq3: - Multiplatform. Binaries available for Windows, Mac and Ubuntu. - It is now a 64-bit program, which can handle larger datasets (genome-scale from multiple individuals). - TreeViewer can show multiple phylogenies in densiTree-like style - Command line tools (e.g vcf2fasta) for integration into pipelines Disclamer: No warranty of any kind is provided - use at your own risk -
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Lung cancer screening panel
Software for predicting probability of lung cancer from VCF file
We have developed a lung cancer screening panel based on the occurrence of specific clonal hematopoietic mutations in peripheral blood samples. The software provided here can be used to predict the probability of cancer from peripheral blood samples. The sequencing data from the blood sample should be first aligned to the GRCh38 reference genome using the Burroughs-Wheeler aligner and variants called using the Mutect2 for variant calling. The resulting VCF file is used as input to the software... -
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Manatee is a web-based gene evaluation and genome annotation tool. Manatee can store and view annotation for prokaryotic and eukaryotic genomes.
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BIGSdb
Software for storing and analysing bacterial sequence data
The Bacterial Isolate Genome Sequence Database (BIGSdb) is a scalable, web-accessible database system designed to store and analyse linked phenotypic and genotypic information in a computationally efficient manner. Sequence data can range from single sequence reads to multiple contigs generated by whole genome sequencing technologies. The system incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences... -
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FungiRegEx
FungiRegEx
This tool is a web-based search engine for regular expressions in the proteomes, all the information is obtained from the JGI (Joint Genome Institute) database through a scraper for all the available species; therefore this tool only considers fungi organisms. In this version, we use React JS in front-end and NodeJS + Express for back-end. Full Documentation Available on: https://victormiguelterronmacias.slite.page/p/J7BJU3hXhd72EJ/FungiRegEx-Software-documentation If you want... -
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CodonU
A python project for analysis of codon usage for gene or genome analys
With CodonU, you can now easily read, manipulate, and analyze various file formats used in this kind of analysis, and generate high-quality graphics suitable for publishing. This open-source project incorporates various statistical measures necessary for codon usage analysis, including codon adaptation index, codon bias index, Gravy score, and correspondence analysis for both nucleotide and protein sequences. Start using CodonU today and see how it can revolutionize your genomics... -
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
123VCF has been developed to make the filtration step of VCF files efficient and more importantly easy to understand. It can be used in the most important step of whole exome/genome sequencing data analysis in the research and also clinical settings. User manual: https://dl.adbioinformatics.net/123VCF/123VCF_Manual.ver2.pdf If you use 123VCF, please cite its paper: Eidi, M., Abdolalizadeh, S., Moeini, S. et al. 123VCF: an intuitive and efficient tool for filtering VCF files. BMC... -
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genppi
GENPPI: standalone software for creating protein interaction networks
Our software GENPPI is efficient because, for example, it creates interaction networks from the central genome of 50 species/lineages of Corynebacterium, with an average size of 2200 genes, in less than 40 minutes, on a conventional computer. Our software is compelling because the interaction networks that it creates reflect evolutionary relationships between species and obtained in Average Nucleotide Identity (ANI) analyzes. Also, It allows the user to define how he intends to explore the PP...