GFinisher: a new strategy to refine and finish bacterial genome assemblies
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of...bly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xm...2170 days ago
Indexcov: fast coverage quality control for whole-genome sequencing
indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potenti...2136 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.2159 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can...2086 days ago
2151 days ago
SimLoRD: A read simulator for third generation sequencing reads
SimLoRD is a read simulator for third generation sequencing reads and is currently...al chromosomes, whose structure is respected when drawing reads. (Simulation of genome rearrangements may be incorpo...2143 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Mulan: Multiple-sequence local alignment and visualization for studying function an...tes identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.2141 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. The program could utilize I... PEP_scaffolder ) for scaffolding genome sequences. The most important...2128 days ago
Ensembl Variation - Calculated variant consequences
For each variant that is mapped to the reference genome, we identify all overlapping Ensembl transcripts. We then use a rule-based approach to predict the effects that each allele of the varia...2125 days ago
SeqMonk:A tool to visualise and analyse high throughput mapped sequence data
SeqMonk is a program to enable the visualisation and an...isualisation of mapped regions against an annotated genome. Flexible quantitation of th...f interest Creation of reports containing data and genome annotation...2124 days ago