Jit
Enthusiast computational biologist with business dream !!!
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NVIDIA and Arc Institute Unveil Evo 2: A Breakthrough AI for DNA Design
By BioStar 590 days agoNVIDIA and the Arc Institute have introduced Evo 2, a groundbreaking AI model designed to understand, predict, and generate DNA sequences. This marks a major advancement in computational biology, offering scientists an unprecedented tool to decode...When Thousands of Bacterial Genomes Become One Giant Map
By LEGE 38 days agoDeveloped by Jérôme Arnoux and colleagues, PANORAMA is a computational tool designed to explore bacterial pangenomes—the complete collection of genetic possibilities found across a species or group of related organisms. Instead of looking at every...The Tree That Learned to Read Genomes
By BioStar 23 days agoA recent study by Webster and Chapman introduces Buscogeny, an open-source bioinformatics pipeline designed to make this process easier. The tool uses BUSCO (Benchmarking Universal Single-Copy Orthologs), which identifies conserved genes that are...Tools and Method for Haplotype phasing !
By Manisha Mishra 2220 days agoHuge amounts of genotype data are being produced with recent technological advances, both from increasingly comprehensive and inexpensive genome-wide SNP microarrays and from ever more accessible whole-genome and whole-exome sequencing methodsUnderstanding Fastqc Output
By Jit 3824 days agowww.bioinformatics.babraham.ac.uk - Understanding Following table and graphs Duplication level kmer profile per base GC content per base N content per base quality per base sequence content per sequence GC content per sequence quality sequence length distribution More at...The "Ifs" and "Buts" of NGS Quality Control and Trimming
By BioStar 639 days agoNGS quality control and trimming are essential steps to ensure reliable and accurate data for analysis. While the "ifs" highlight the clear benefits of these steps, the "buts" remind us of the potential pitfalls. By adopting best practices and...iSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 2422 days agogithub.com - iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering,...CNIDARIA: fast, reference-free phylogenomic clustering
By Shruti Paniwala 3762 days agogithub.com - Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes...Cactus: a reference-free whole-genome multiple alignment program
By Jit 2610 days agogithub.com - Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111 Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should...GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
By Abhimanyu Singh 3421 days agogithub.com - GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which...
