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ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
By BioStar 2785 days agogithub.com - The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed...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...LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
By Neel 1869 days ago Comments (1)academic.oup.com - LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that...MAKER
By Jitendra Narayan 3831 days ago Comments (1)www.yandell-lab.org - MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats,...fragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 3005 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
By Abhimanyu Singh 2833 days agoancestralgenomes.org - Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these ‘fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species...JCVI utility libraries
By Jit 1914 days agogithub.com - Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.ONT assembly and Illumina polishing pipeline
By Jit 3177 days agogithub.com - This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps...dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
By Rahul Nayak 3167 days agogithub.com - dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs...BUSCO
By Jitendra Narayan 3831 days agohttp://busco.ezlab.org/ - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at http://busco.ezlab.org/
