Results for "Bioinformatics"
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MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-ini...Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, MAKER, Genome, Annotation, Pipeline, NGS, Assembly
2993 days ago
- Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at http://busco.ezlab.org/
Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, BUSCO, Genome, Annotation, Pipeline, NGS, Assembly, Orthologs
2993 days ago
- RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome. It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between strains and even different species, like Plasmo...
Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, RATT, Genome, Annotation, Pipeline, NGS, Assembly
2993 days ago
- Tools to create plots showing N-statistics for genome assemblies More at https://github.com/dentearl/n50PlottingTools
Tags: Bioinformatics, Computational Biology, Education, Plot, N50, NGS
2992 days ago
- Convenient conversions between genome assemblie. The liftover package makes it easy to remap genomic coordinates to a different genome assembly. More at https://github.com/aaronwolen/liftover https://www.bioconductor.org/help/workflows/liftOver/
Tags: Bioinformatics, Computational Biology, Education, liftover, N50, NGS, Assembly, Genomics
2992 days ago
- CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig,...
Tags: Bioinformatics, Computational Biology, Education, CrossMap, N50, NGS, Assembly, Genomics
2992 days ago
- Pilon is a software tool which can be used to: Automatically improve draft assemblies Find variation among strains, including large event detection Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read ...
Tags: Bioinformatics, Computational Biology, Education, Pilon, N50, NGS, Assembly, Genomics
2992 days ago
- Spines Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets ...
Tags: Bioinformatics, Spines, Satsuma, Synteny, Papaya, SLAP, Tools
2991 days ago
- flo - same species annotations lift over pipeline Lift over is the process of transferring annotations from one genome assembly to another. Usually lift over is done because there is a new, improved genome assembly for the species and good quality annotations (maybe manually curated or experimen...
Tags: Bioinformatics, Flo, Liftover, Annotation
2990 days ago
- NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use the API for NCBI Remap. More at http://www.ncbi...
Tags: Bioinformatics, NCBI, NCBI Remap, Liftover, Annotation
2989 days ago
