Search Results for "genome" - Page 2
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Showing 521 open source projects for "genome"
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A tool to estimate trends in recent effective population size trajectories using genome-wide SNP data.
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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 and CN characteristics through various parameters that let on the creation of customized interaction networks. ... -
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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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A fungal genome annotation pipeline (funnote) integrated by CAIQ (Chinese Academy of Inspection and Quarantine). ## prerequisites 1. skewer (https://github.com/relipmoc/skewer) 2. BLAST (https://blast.ncbi.nlm.nih.gov/) 3. DIAMOND (https://github.com/bbuchfink/diamond) 4. funannotate (https://github.com/nextgenusfs/funannotate) 5. InterProScan (https://github.com/ebi-pf-team/interproscan) 6. emapper (https://github.com/eggnogdb/eggnog-mapper)
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sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
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genome-wb3-asm
A Genetic Algorithm Library written in Amiga Workbench 3.x assembler
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miRPV
miRPV: An automated pipeline for miRNA Prediction and Validation in si
miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence. System Requirement CPU: AMD64 (64bit) Memory: 2Gb RAM Storage: 5Gb Ubuntu 18.04 -
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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 and accuracy in metagenomic assemblies. ... -
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Covidex
Ultra fast and accurate subtyping tool of viral genomes.
...It is a shiny app that allows fast and accurate classification of viral genomes in pre-defined clusters. If more than 1000 sequences are loaded the tool will run in multithread mode. Capable of classifying 16000 genome sequences in less than a minute (AMD Ryzen 7 1700 8-core Processor 3 GHz) For a Web-based version of the app (only for small datasets: 100 seqs max) please go to http://covidex.unlu.edu.ar If you use Covidex please consider citing the following preprint: https://biorxiv.org/cgi/content/short/2020.08.21.261347v1 If you think my work is useful you can buy me a coffee! ... -
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PhaseDel
Phasing-based somatic deletion caller from single-cell WGS data
PhaseDel is a Java-based variant caller designed for detecting somatic deletions from single-cell whole-genome sequencing (scWGS) data. It is highly specialized for discriminating genuine somatic focal deletions (several bases to kilo-bases in length) from excessive SV-like artifacts, which are inevitably occurring during single-cell whole-genome amplification. PhaseDel accurately detects such true deletions based on the linkage information between deletion breakpoints and nearby germline heterozygous SNP sites. ... -
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PAN2HGENE, a computational tool that allows identification of gene products missing from the original genome sequence, with automated comparative analysis for both complete and draft genomes, can be used to address this limitation. In this study, PAN2HGENE was used to identify new products, resulting in altering the alpha value behavior in the pangenome without altering the original genomic sequence. Our findings indicate that this tool represents an efficient alternative for comparative analysis, with a simple and intuitive graphical interface.
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis. ... -
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. ... -
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mimicree2
Genome-wide forward simulations of evolving populations
MimicrEE2: genome-wide forward simulations of adapting populations. For a detailed description, a manual, several walkthroughs and the validation see https://sourceforge.net/p/mimicree2/wiki/Home/ -
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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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GenoCline
GenoCline is a free Java software for genetic cline analysis
Identification of clines from allele frequency or genome-wide databases. Angular transformation. Sigmoid function. Parameterization of a cline: orientation, Pearson’s product-moment correlation coefficient, linear and sigmoid regression and coefficient of determination. Graphical representation of the cline. Confidence limits. Spatial autocorrelation. Moran's index. Isolation by distance. -
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GENET-CNV
Integrated DNA copy number variation and gene expression analysis
The Boolean implication networks outperformed Bayesian networks, Pearson’s correlation networks, and other Boolean networks in constructing genome-scale co-expression networks evaluated with comprehensive biological pathways and Gene Ontology in MSigDB. References: Guo NL, Wan YW. Pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival. Artificial Intelligence in Medicine 2012 Jun;55(2):97-105. Ye Q, Singh S, Qian PR, Guo NL. ... -
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miRDP2
Accurately and fast analyzing microRNAs transcriptome in plants
...It is adopted from miRDeep-P (miRDP) with new strategies and overhauled algorithm. We have tested miRDP2 to analyze miRNA transcriptomes in such plants with gradually increased genome size as Arabidopsis, rice, tomato, maize and wheat. Compared with miRDeep-P and several other computational tools, miRDP2 processed NGS data with superior speed. By incorporating newly updated plant miRNA annotation criteria, the accuracy of miRDP2 is also markedly improved. Our results demonstrate miRDP2 as a fast and accurate tool for analyzing the miRNA transcriptome in plants. ... -
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GMATA software for Genomic SSR marker
Genome-wide Microsatellite Analyzing Toward Application: GMATA
...GMATA is accurate, sensitive and fast. It was designed to process large genomic sequence data sets, especially large whole genome sequences. In theory, genomes of any size can be analyzed by GMATA easily. Software GMATA works on sever, desktop or even laptop, and it can run in graphic interface with just clicks or run in command line or in automated pipeline. It is also cross-platform and supports Unix/Linux, Win and Mac. Results from software GMATA can be directly graphically displayed with genome or gene features in Gbrowser and easily integrated with any genomic database. -
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SingleCellSeqCNV
Detection of Copy Number Alterations by Single Cell Sequencing
Detection of Copy Number Alterations by Single Cell Sequencing Kristin A. Knouse, Jie Wu and Angelika Amon, Assessment of megabase-scale somatic copy number variation using single cell sequencing. Genome Research, 2016. gr. 198937.115 Kristin A Knouse, Jie Wu, Charles A Whittaker and Angelika Amon. Single cell sequencing reveals low levels of aneuploidy across mammalian tissues. Proceedings of the National Academy of Sciences, 2014. 111(37):13409-13414. -
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RNA@
RNA annotation tool
...The algorithm principle is to encode a data set of nucleotide sequences into a Finite State Machine able to recognize every occurrence of every nucleotide sequence into a genome in a single read of the genome. As nucleotide sequence data set, RNA@ uses a collection of about 300,000 RNA deposited into the NCBI. These RNA are automatically collected from about 25,000 complete deposited genomes. You will find at https://drive.google.com/file/d/1lEj5SSHpQSv54nOroxBcS_jvLFRIKNmm/view?usp=sharing" the RNA re-annotated by RNA@ for 30,558 genomes of Archaea and Bacteria (all the archaea and bacteria genomes marked as "Complete Genomes" or "Chromosome" among the genomes deposited in the NCBI day June 06 of 2021. ... -
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LDhelmet
Fine-scale recombination rate estimation.
...The source code and the recombination maps for two populations of Drosophila melanogaster are available for download. Reference: Andrew H. Chan, Paul A. Jenkins, Yun S. Song (2012). Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster. PLoS Genet 8(12): e1003090. doi:10.1371/journal.pgen.1003090 -
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MitoSAlt
Identification of mitochondrial structural alterations
MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided. -
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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
