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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (167 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (624 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (785 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (837 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Bio7: an integrated development environment for ecological modeling, scientific image analysis and...
By Nidhi Rajput 1750 days agohttps://bio7.org/home-2/ - The application Bio7 is an integrated development environment for ecological modeling, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge...Free Genomics data !
By BioStar 1750 days agowww.darwintreeoflife.org - The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane...Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit,...
By Neel 1751 days agowww.phrap.org - Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence...shinyCircos: an R/Shiny application for interactive creation of Circos plot
By Jit 1751 days ago150.109.59.144 - shinyCircos, a graphical user interface for interactive creation of Circos plot. shinyCircos can be easily installed either on computers for personal use or on local or public servers to provide online use to the community. Furthermore, various...MEC: Contig Misassembly Correction
By BioStar 1753 days agogithub.com - MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on...Tadpole: an assembler, error-corrector, and read-extender
By BioStar 1753 days agojgi.doe.gov - Tadpole is a kmer-based assembler, with additional capabilities of error-correcting and extending reads. It does not do any complicated graph analysis or scaffolding, and therefore, is not particularly good for diploid organisms. Tadpole is...QuorUM: An Error Corrector for Illumina Reads
By BioStar 1753 days agowww.genome.umd.edu - We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is...Musket - a multistage k-mer spectrum based corrector
By BioStar 1753 days agomusket.sourceforge.net - Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 1753 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...Nanopore adaptor !
By Jit 1755 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads....
