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Jabba: Hybrid Error Correction for Long Sequencing Reads
By Jit 2983 days agogithub.com - Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph...NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
By BioStar 2599 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...Understanding HiFi Reads !
By Rahul Nayak 1444 days agopacb.com - While little public data is available for either of the new synthetic long read approaches, Illumina showed an example comparison earlier this year at the Festival of Genomics & Biodata conference (FoG 2022). In the IGV screenshot...Trust But Verify: Sequencing Your Cell Lines Might Reveal an Uninvited Guest
By LEGE 277 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,...Mauve: a system for constructing multiple genome alignments in the presence of large-scale...
By Jit 3360 days agodarlinglab.org - Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of...SVfinder: Tool for detecting genomic rearrangement form DNA-seq data
By Robert M Willioms 3005 days agogithub.com - SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.CNIDARIA: fast, reference-free phylogenomic clustering
By Shruti Paniwala 3551 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...Merqury: reference-free quality and phasing assessment for genome assemblies
By Jit 2100 days agogithub.com - Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality...BioGPS
By Anjana 3575 days agobiogps.org - A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function. http://biogps.org/#goto=welcomeJPred4: A Protein Secondary Structure Prediction Server
By Poonam Mahapatra 2990 days agowww.compbio.dundee.ac.uk - JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure...
