Results for "Rare variants"
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Recovery of complete genomes from metagenomes
This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome sequences of rare, un...2313 days ago
- Breakpointer is a fast tool for locating sequence breakpoints from the alignment of...signatures created by insertion/deletions (indels) or more complex structural variants(SVs)....
2146 days ago
- Download and install MUMmer Align your assembly to a reference genome using nucmer...esents an anchor for determining if a sequence is unique enough to safely call variants from, which is an alternative...
2144 days ago
- SRBreak is a read-depth and split-read package written in R for identifying copy-number variants in next-generation sequencing...
2174 days ago
LAMSA: fast split read alignment with long approximate matches
...ver thousands of base-pairs). LAMSA takes takes the advantage of the rareness of SVs to implement a spe...DP)-based split alignment approach to handle the large or non-co-linear variants. We benchmarked LAMSA with...2174 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA seque...s time HapCUT2 is for diploid organisms only. VCF input should contain diploid variants. If you use HapCUT2 in you...2174 days ago
- Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somati...
2161 days ago
WhatsHap: fast and accurate read-based phasing
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or hapl...es of reads It phases SNVs, indels and even “complex” variants (such as TCG →...2161 days ago
gSearch: a fast and flexible general search tool for whole-genome sequencing
gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner.2091 days ago
NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV ca...2091 days ago
