HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...ligation (Hi-C) reads high-coverage sequencing (>40x coverage-per-SNP) using above technologies combinations of the above technologies (e.g. scaffold long reads with Hi-C reads)...2183 days ago
TULIP - The Uncorrected Long read Integration Pipeline
...r implementations are likely to follow. Tulipseed takes as input alignments files of long reads to sparse short seeds, and outputs a graph and scaffold structures.2183 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version...blication which describes the methods used for scaffolding. Ghurye, J., Pop, M., K...n, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies us...2152 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes....s or other Protein-based approaches (for instance, PEP_scaffolder ) for scaffolding geno...2068 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
...bred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable results: super-scaffold N50 values in the range of do...1721 days ago
SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:1542 days ago
CSAR-web: a web server of contig scaffolding using algebraic rearrangements
...s a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the c...related organism. CSAR-web can serve as a convenient and useful scaffolding tool allowing the users to...1487 days ago
RagTag: a collection of software tools for scaffolding and improving modern genome assemblies
RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: Homology-based misassembly correction Homology-based assembly scaffolding and patching Scaffold merging968 days ago