GFinisher: a new strategy to refine and finish bacterial genome assemblies
...is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of...ew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xm...2171 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 p...2137 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.2160 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...2087 days ago
2152 days ago
SimLoRD: A read simulator for third generation sequencing reads
...randomly generated with a given GC content. It can consist of several chromosomes, whose structure is respected when drawing reads. (Simulation of genome rearrangements may be incorpo...2144 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
...n be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.2142 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
...novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize I...(for instance, PEP_scaffolder ) for scaffolding genome sequences. The most important...2129 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...2126 days ago
SeqMonk:A tool to visualise and analyse high throughput mapped sequence data
...tion and analysis Visualisation of mapped regions against an annotated genome. Flexible quantitation of th...ta to find regions of interest Creation of reports containing data and genome annotation...2125 days ago