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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (332 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (789 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (950 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 (1002 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 1829 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1832 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
By Jit 1838 days agogithub.com - FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and...WEGO : simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation...
By BioStar 1850 days agowego.genomics.org.cn - WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. As the GO vocabulary became more and more popular, WEGO was widely adopted and used in many...CSAR-web: a web server of contig scaffolding using algebraic rearrangements
By BioStar 1853 days agogenome.cs.nthu.edu.tw - CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism. CSAR-web can...Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
By BioStar 1854 days agogithub.com - Dahak is a software suite that integrates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak software suite will perform various steps in metagenomic analysis workflows including data pre-processing, metagenome assembly,...QuartataWeb: user-friendly server developed for polypharmacological and chemogenomics analyses.
By Neel 1861 days agoquartata.csb.pitt.edu - Data on protein-drug and protein-chemical interactions are rapidly accumulating in databases such as DrugBank and STITCH. These data usually reflect observed interactions, while the lack of data for a given protein-drug/chemical pair...HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from...
By BioStar 1866 days agogithub.com - HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. More...Coronavirus Resources !
By Neel 1868 days ago Comments (15)bigd.big.ac.cn - 2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the GISAID, NCBI, NMDC and CNCB/NGDC. It also incorporates a wide range of relevant information including scientific...tinycov: standalone command line utility written in python to plot coverage from a BAM file
By Jit 1871 days agogithub.com - Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plotter. To install the stable version: pip3 install --user...
