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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (169 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (625 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (786 days ago): Sequencing coverage is defined as the average number of reads that covers...
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flo
By Jitendra Narayan 3210 days agogithub.com - 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...Spines
By Jitendra Narayan 3211 days agowww.broadinstitute.org - 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,...Pilon
By Rahul Nayak 3212 days agogithub.com - 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...CrossMap
By Jitendra Narayan 3212 days agocrossmap.sourceforge.net - 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...liftover
By Jitendra Narayan 3212 days ago Comments (1)github.com - Convenient conversions between genome assemblie. The liftover package makes it easy to remap genomic coordinates to a different genome assembly. More at...n50PlottingTools
By Jit 3212 days agogithub.com - Tools to create plots showing N-statistics for genome assemblies More at https://github.com/dentearl/n50PlottingToolsRATT
By Jitendra Narayan 3213 days agoratt.sourceforge.net - 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...BUSCO
By Jitendra Narayan 3213 days agohttp://busco.ezlab.org/ - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at http://busco.ezlab.org/MAKER
By Jitendra Narayan 3213 days ago Comments (1)www.yandell-lab.org - 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,...Recombination detection tool
By Jit 3218 days ago Comments (2)github.com - A program to detect recombination hotspots using population genetic data. More at https://github.com/auton1/LDhot
