Indexcov: fast coverage quality control for whole-genome sequencing
indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples w...eal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Inde...2133 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.2155 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 t...erform downstream annotation using ANNOVAR and disease gene discovery using Phenoly...2155 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
...ants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well...on and copy number pipelines, and h...o;PureCN: Copy number calling and SNV classification using targeted short read sequencing.” Source Code for...2153 days ago
FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
FMLRC, or FM-index Long Read Corrector, is a tool for performing...hybrid correction of long read sequencing using the BWT and FM-index of short-read seque..., FMLRC will build an FM-index and use that as an implicit de Bruijn gr...quency k-mers in the long read and replacing them with the closest matc...2151 days ago
NanoPack: visualizing and processing long-read sequencing data
The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code...ster/nanopack, together with links to separate scripts and t...ntation. The scripts are compatible with Linux, Mac OS and the MS...2151 days ago
2147 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de n...e potential to achieve better and m...mong all competing algorithms and highest accuracy when most of the ba...2141 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
Second generation sequencing technologies paved the way to an e...ads are difficult to assemble and often lead to highly fragment...s the ones produced by PacBio sequencing technology, using high-qualit...the edit score to a long read and extending corrected regions by local...2141 days ago
SimLoRD: A read simulator for third generation sequencing reads
SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacif...Reads are simulated from both strands of a provided or randomly ge...can be read from a FASTA file or random...ng a fixed length Quality values and number of passes depend on fragment...2139 days ago