Nanopolis: polish a genome assembly
...sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below). Quickstart http://...2109 days ago
sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
Required python modules biopython intervaltree numpy scipy tqdm PyYAML1999 days ago
1964 days ago
Biotite: A general framework for computational biology
...thon. Biotite consists of four sub packages: sequence, structure, databases, and application. The sequence and structure modules serve for the analysis of seq...1964 days ago
Versatile genome assembly evaluation with QUAST-LG
...ES for all): Significant speedup achieved by both use of new fast aligner (minimap2) and the refactoring of alignment analyzing modules New k-mer-based completeness...1960 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
...ox and TSRs and reliable LTRs are selected. Next, LTR_FINDER tries to identify PBS, PPT and RT inside LTR pairs by build-in aligning and counting modules. RT identification includes a...1938 days ago
OMTools: a software package for visualizing and processing optical mapping data
...dle and explore large-scale optical mapping profiles. OMTools includes modules for visualization (OMView), data processing and simulation. These modules together form an accessible a...1863 days ago
NextDenovo: string graph-based de novo assembler for TGS long reads
...mbly, the per-base error rate is about 97-98%, to further improve single base accuracy, please use NextPolish. NextDenovo contains two core modules: NextCorrect and NextGraph. N...1581 days ago
flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
...sus and error-prone sequences, FlexiDot harbors routines for strict and relaxed handling of mismatches and ambiguous residues. The custom shading modules facilitate dotplot interpreta...1471 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together...885 days ago