Jit
Enthusiast computational biologist with business dream !!!
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Maq: Mapping and Assembly with Quality
By Jit 3395 days agomaq.sourceforge.net - Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/....Understanding PacBio
By Jitendra Narayan 3301 days agogithub.com - This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3282 days agoStructural variation caller tools using long readsQuorUM: An Error Corrector for Illumina Reads
By Jit 3044 days agojournals.plos.org - Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read...HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
By Abhimanyu Singh 2625 days agogithub.com - HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read...Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 1879 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.Trust But Verify: Sequencing Your Cell Lines Might Reveal an Uninvited Guest
By LEGE 280 days agoHigh-throughput sequencing has become indispensable in cell biology, enabling detailed insights into chromatin structure, gene expression, and regulatory dynamics. Yet, when faced with unexpectedly low mapping rates to the human genome,...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 2882 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...MSAProbs - Parallel and accurate multiple sequence alignment
By Neel 2436 days agomsaprobs.sourceforge.net - MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior...CLARK: Fast, accurate and versatile sequence classification system
By Jit 2215 days agoclark.cs.ucr.edu - CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to...
