BEAP: Blast Extension and Assembly Program
...or SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. https://...2214 days ago
D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome an.... We use minimap version 2 to align the two genomes. Then, the PAF file is parse...2214 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
...ast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve t...were almost completely recovered and equivalent to those in a complete genome, especially for long proteins...2213 days ago
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
RestrictionDigest can simulate the reference genome digestion and generate comprehe...election process. It can also analyze multiple genomes at one run and generates con...comparison of enzyme(s) performance across the genomes. For more information, pl...2213 days ago
2211 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
...tion tools. MECAT can be used for effectively de novo assemblying large genomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT takes 9.5 days to assemble a human genome based on 54x SMRT data, which...2245 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
...bility map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further informatio..., Kitzman JO, Shendure J#. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin...2242 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
...contiguity information for scaffolding de novo genome assemblies. FragScaff is comp...port robust, accurate chromosome-scale de novo genome assemblies without the need f...o, long-range sequence information for de novo genome assembly via transposase cont...2242 days ago
2241 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...esearch, please cite: Edge, P., Bafna, V. & Bansal, V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res. gr.213462.116 (2016). do...2241 days ago