Jit
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Minipolish: A tool for Racon polishing of miniasm assemblies
By BioStar 1810 days agogithub.com - Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long...merqury: Evaluate genome assemblies with k-mers
By Jit 1597 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...Syri compares alignments between two chromosome-level assemblies and identifies synteny and...
By Shruti Paniwala 899 days agogithub.com - Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.PBSuite: Software for Long-Read Sequencing Data from PacBio
By Jit 2819 days agosourceforge.net - PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The...proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
By Jit 2507 days agogithub.com - proovread : large-scale high-accuracy PacBio correction through iterative short read consensus outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity (http://dx.doi.org/10.1093/bioinformatics/btu392) is easy to...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2368 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2263 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
By BioStar 2196 days agogithub.com - Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source...AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 1343 days agogithub.com - AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2803 days agoStructural variation caller tools using long reads
