BioStar
Bioinformatician
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YAHA
By Jit 3335 days agowww.ncbi.nlm.nih.gov - YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments....QuorUM: An Error Corrector for Illumina Reads
By Jit 3043 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...NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
By BioStar 2601 days agogithub.com - NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file...Common steps for reads mapping !
By BioStar 1096 days agoMapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis.Rolf Backofen Lab
The research interest of this group include constraint programming, structure prediction in simplified protein models, investigation of protein energy landscapes, detection of RNA sequence/structure motifs, prediction and evaluation of alternative...RNA Sequencing Helps Identify Functional Variants from GWAS
By Andaleeb 4489 days agoschizophreniaforum.org - For Alzheimer’s and other complex disorders, mining the genome for disease-associated variants is no longer the obstacle. The challenge nowadays is figuring out how the identified loci relate to disease. As reported last month in Nature and...Barrnap: Bacterial ribosomal RNA predictor
By Abhimanyu Singh 3223 days agogithub.com - Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). It takes FASTA DNA sequence as input, and write GFF3 as output....SEASTAR: Systematic Evaluation of Alternative STArt site in RNA
By BioStar 2034 days agogithub.com - SEASTAR (Systematic Evaluation of Alternative STArt site in RNA) is a software package for Transcription Start Site (TSS) identification and quantification using only RNA-seq data. It assembles novel TSSs based only on RNA-Seq data and merges them...Understanding RNA-Seq Normalization Methods: TPM vs. FPKM vs. CPM
By Neel 453 days agoChoosing the right normalization method depends on the specific objectives of your RNA-Seq analysis. TPM’s proportionality and robustness make it the preferred choice for most applications, while CPM serves well for differential expression...CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies
By Rahul Nayak 2993 days agohttps://cblab.org/camsa/ - CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license. Main features: works with any number of...
