ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...C is a pipeline which facilitates iterative, reference guided de novo asse...should assemble together. Reducing/removing reference bias as compared to mapping b...e specific content and a set of semi-similar reference targets is available to initi...2162 days ago
GFinisher: a new strategy to refine and finish bacterial genome assemblies
...tify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar Ge...-i target_contigs.fasta \ -ds alternative_assemblies.fasta -ref reference.fasta \ -o outputDirect...2162 days ago
Bokeh: An interactive visualization library that targets modern web browsers for presentation
...the User Guide. To see examples of how you might use Bokeh with your own data, check out the Gallery. A complete API reference of Bokeh is at Reference Guide. If you are interested...2146 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 substitut...ingle folder. It can then take a set of Snippy results using the same reference and generate a core SNP align...2077 days ago
SimLoRD: A read simulator for third generation sequencing reads
...ly focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference can be read from a FASTA file...2135 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 t...2116 days ago
Rebaler: program for conducting reference-based assemblies using long reads.
Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences...2108 days ago
KAST: Perform Alignment-free k-tuple frequency comparisons from sequences
Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.2106 days ago
BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
...the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on th...2071 days ago
QUAST-LG: Versatile genome assembly evaluation
...UAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes releva...he theoretical optimum, and how far this optimum is from the finished reference. AVAILABILITY AND IMPLEMENTA...2071 days ago