LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including sou...2203 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
...ces between the content of different pools as a source of contiguity information for scaffolding de novo genom...blies without the need for laborious in vivo cloning steps. Further information about fragScaff, including so...2203 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
...olding. Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact information. BMC genomics, 18(1), 527. Li...2171 days ago
CGView - Circular Genome Viewer
...imary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are sup...2166 days ago
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
...atively, if your scientific question is focused on only one aspect of the data (e.g. breakpoints), many reads can be removed without losing the information relevant to the problem. &nb...2060 days ago
2060 days ago
BASE: a practical de novo assembler for large genomes using long NGS reads
...orm the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality co...2045 days ago
vcfR: a package to manipulate and visualize VCF data in R
...d write to VCF files. Once VCF data is read into R a parser function extracts matrices from the VCF data for use with typical R functions. This information can then be used for quality...2039 days ago
Referee: Genome assembly quality scores
...asure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a...2029 days ago
BLAST options, setting and defaults
...LAST searching can be found at the NCBI BLAST Help Manual. For a theoretical overview of BLAST, see the NCBI BLAST Course. Additional information can be found in the BLAS...1993 days ago