Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
...lished genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contami...2369 days ago
IONiseR: tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer
...ed to provide tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer. It includes a functions to generate a number plots for examining the stati...2369 days ago
DRAWID: user-friendly Java software for chromosome measurements and idiogram drawing
"DRAWID has number of advantages including a user-friendly interactive interface, possibility...me and FISH/GISH/banding signal measurement and idiogram drawing as well as number of useful functions facilitat...2365 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
...gram allows the user to design a metagenome by specifying the number of genomes present at differe...then to collect reads from the metagenome using a simulation of a number of different sequencing techn...2358 days ago
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. A...2342 days ago
CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies
... Assemblies, distributed both as a standalone software package and as Python library under the MIT license. Main features: works with any number of scaffold assemblies in de-...2334 days ago
Seal: SEquence ALignment evaluation suite
...plying alignment tools to the genome and the reads through a standardized interface. Parsing the output of the alignment tool and calculating the number of reads that were correctly...2328 days ago
Genome assembly stats plotting
A de novo genome assembly can be summarised b y a number of metrics, including: Overall assembly length Number of scaffolds/contigs Length of longest scaffold/contig Scaffold/contig N50 and N90As...2272 days ago
Reference-free prediction of rearrangement breakpoint reads
...eak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When ap...2264 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
...uation framework considers the optimal assignment of contigs in the output scaffolding to contigs in the reference scaffolding in the sense of the number of correct links. ht...2251 days ago