Bulbul
Bioinformatician
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QUAST-LG: Versatile genome assembly evaluation
By Jit 2905 days agocab.spbu.ru - QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we...DeCoSTAR - Detection of Co-evolution
By Jit 3464 days agopbil.univ-lyon1.fr - DeCoSTAR is a software which aims at reconstructing ancestral gene or genome organizations, in the form of sets of neighborhood relations -adjacencies- between pairs of ancestral genes or gene domains.Ancestral genes or domains are deduced from...CANU genome assembly parameters !
By Rahul Nayak 2831 days agoChoose the appropriate parameters to run Canu and run it.SSPACE
By Jit 3443 days agowww.baseclear.com - SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or...CAR: Reconstructing Contiguous Regions of an Ancestral Genome
By Abhimanyu Singh 3430 days agowww.bx.psu.edu - We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map...BlobToolKit: A toolkit for genome assembly QC
By Jit 2421 days agoblobtoolkit.genomehubs.org - Filtering raw genomic datasets is essential to avoid chimeric assemblies and to increase the validity of sequence-based biological inference. BlobToolKit extends the BlobTools1/Blobology2 approach to simplify interactive and reproducible...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 2351 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...Illumina based assembly pipeline steps !
By Surabhi Chaudhary 1763 days agoGenome assembly pipeline !MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
By Abhi 1129 days agogithub.com - MitoHiFi v3.2 is a python pipeline distributed under MIT License ! MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project...liftover
By Jitendra Narayan 3894 days ago Comments (1)github.com - Convenient conversions between genome assemblie. The liftover package makes it easy to remap genomic coordinates to a different genome assembly. More at...
