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ALE: a Generic Assembly Likelihood Evaluation Framework for Assessing the Accuracy of Genome and...
By Neel 3179 days ago Comments (1)sc932.github.io - Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and...Maq: Mapping and Assembly with Quality
By Jit 2969 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/....Jvarkit : Java utilities for Bioinformatics
By Jit 2406 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for BioinformaticsSpeedSeq
By Jit 2910 days agogithub.com - A flexible framework for rapid genome analysis and interpretation C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2856 days agoStructural variation caller tools using long readspbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2421 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...Understanding HiFi Reads !
By Rahul Nayak 1021 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...CoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2333 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....GABi
GABi Research The major researching fields defined as the GABi scope are described next: Sequence Analysis Protein Structure Prediction Comparative Genomics Functional Analysis of Residues on Protein Families Gene/Protein...The genome factory !!!
By Madhvan Reddy 4010 days agoWorld’s first $1,000 genome enables ‘factory’ scale sequencing for population and disease studies
