Nanopolis: polish a genome assembly
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopol...culate an improved consensus sequence for a draft genome assembly, detect base modific...call SNPs and indels with respect to a reference genome and mor...2171 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of:...approaches. The software is designed to work in situations where a whole-genome assembl...2171 days ago
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 GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes refere...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, recogn...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.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...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 focused on the Pacific Bioscie...chromosomes, whose structure is respected when drawing reads. (Simulation of genome rearran...2144 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution Mulan (http://mul...identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotat...2142 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 Illumina Paired-end RNA...nstance, PEP_scaffolder ) for scaffolding genome sequenc...2128 days ago