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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (166 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (622 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (783 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 (836 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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auN: a new metric to measure assembly contiguity
By Jit 843 days agolh3.github.io - Given a de novo assembly, we often measure the “average” contig length by N50. N50 is neither the real average nor median. It is the length of the contig such that this and longer contigs cover at least 50% of the assembly. A...Monkeypox virus isolate MPXV_USA_2022_MA001, complete genome
By Jit 849 days agowww.ncbi.nlm.nih.gov - LOCUS ON563414 197205 bp DNA linear VRL 30-MAY-2022 DEFINITION Monkeypox virus isolate MPXV_USA_2022_MA001, complete genome. ACCESSION ON563414 VERSION ON563414.3 KEYWORDS . SOURCE Monkeypox virus...Human Complete Genome
By Shruti Paniwala 869 days agowww.science.org - Telomere-to-telomere consortium We have sequenced the CHM13hTERT human cell line with a number of technologies. Human genomic DNA was extracted from the cultured cell line. As the DNA is native, modified bases will be preserved. The data includes...htop explained
By Jit 870 days agopeteris.rocks - For the longest time I did not know what everything meant in htop. I thought that load average 1.0 on my two core machine means that the CPU usage is at 50%. That's not quite right. And also, why does it say 1.0? I decided to look...JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges
By Shruti Paniwala 873 days agogithub.com - This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine...InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams
By Jit 876 days agowww.interactivenn.net - InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are...ChEMBL
By Shruti Paniwala 883 days agowww.ebi.ac.uk - ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.Choosing the Right NGS Sequencing Instrument for Your Study
By Neel 891 days agogenohub.com - The right sequencing instrument for your study depends on your project goal. Setting aside turnaround time and price, it essentially comes down to the numbers of reads and read length you need for your experiment. Below, we've described and compared...Syri compares alignments between two chromosome-level assemblies and identifies synteny and...
By Shruti Paniwala 905 days agogithub.com - Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
By Shruti Paniwala 911 days agogitlab.com - CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of other tools in order to get an improved precision and recall. Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It...
