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ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
By LEGE 819 days agogithub.com - ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate...VICUNA: a software tool that enables consensus assembly of ultra-deep sequence derived from diverse...
By biogeek 2171 days agowww.broadinstitute.org - VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in...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...TRITEX sequence assembly pipeline for Triticeae genomes
By Jit 2542 days agotritexassembly.bitbucket.io - The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable...GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
By Jit 3005 days agogithub.com - This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this...SeqMonk:A tool to visualise and analyse high throughput mapped sequence data
By Jit 2885 days agowww.bioinformatics.babraham.ac.uk - SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic...Mulan: MUltiple sequence Local AligNment and conservation visualization tool
By Rahul Nayak 3303 days agomulan.dcode.org - Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It...iRNAD: a computational tool for identifying D modification sites in RNA sequence
By Abhimanyu Singh 2638 days agolin-group.cn - iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3164 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...SDA: Long-read sequence and assembly of segmental duplications
By Jit 2710 days agowww.nature.com - Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of...
