Jit
Enthusiast computational biologist with business dream !!!
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QUAST-LG: Versatile genome assembly evaluation
By Jit 2841 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...CANU genome assembly parameters !
By Rahul Nayak 2767 days agoChoose the appropriate parameters to run Canu and run it.gbtools: Interactive Visualization of Metagenome Bins in R
By Jit 3418 days agojournal.frontiersin.org - We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of...CONTIGuator !
By BioStar 2497 days agosourceforge.net - CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).BlobToolKit: A toolkit for genome assembly QC
By Jit 2357 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 2287 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...Eugene V. Koonin Lab
Interested in understanding the evolution of life. To obtain glimpses of such understanding, we employ existing and new methods of computational biology to perform research in several major...Illumina based assembly pipeline steps !
By Surabhi Chaudhary 1699 days agoGenome assembly pipeline !MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
By Abhi 1065 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...CrossMap
By Jitendra Narayan 3830 days agocrossmap.sourceforge.net - CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly...
