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Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare. ISCompare: a new tool for the identification of differentially located insertion sequences on bacteria. Bacterial genomes are composed by a core and an accessory genome.

A multi-level clustering scheme for population assignments based on core genome MLST. HierCC (Hierarchical clustering of cgMLST). HierCC is a multi-level clustering scheme for population assignments based on core genome Multi-Locus Sequence Types (cgMLSTs). HierCC has been implemented in EnteroBase since 2018.

This tool is a scaffolder. The input is a contig file and a set of BAM files from mapping paired-ends and/or mate-pair reads to the contigs, and the output are scaffolds, i.e., the contigs linked and oriented. It is both fast and accurate. Careful estimation of the gaps between contigs, many other scaffolders have seriously biased estimation. Novel treatment of paired-end contamination in mate-pair libraries, which identifies that some links in the MP data are better treated as PE.

Fast Hybrid Assembly of Long Reads. HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample. HASLR is capable of assembling large genomes on a single computing node. Our experiments show that it can assemble a CHM1 human dataset in less than 10 hours using 64 CPU threads.

A probabilistic method for filling gaps in genome assemblies.

DepthSizer: Read-depth based genome size prediction. Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C.

Fast and lightweight assembly-guided scaffolding using minimizer graphs. Scaffolding draft assemblies using reference assemblies and minimizer graphs. ntJoin takes a target assembly and one or more 'reference' assembly as input, and uses information from the reference(s) to scaffold the target assembly. The 'reference' assemblies can be true reference assembly builds, or a different draft genome assemblies.

An accurate and contiguous phasing method for polyploids. Ploidy agnostic phasing pipeline and algorithm. nPhase is a ploidy agnostic tool developed in python which predicts the haplotypes of a sample that was sequenced by both long and short reads by aligning them to a reference. It should work with any ploidy.

Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL. Large genome reassembly based on Hi-C data, continuation of GRAAL. Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries. This work is under continuous development/improvement - see GRAAL for information about the basic principles. sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal. Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)

CulebrONT is a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes.

An end-to-end solution for high-quality complete bacterial genome construction. microPIPE: a pipeline for high-quality bacterial genome construction using ONT and Illumina sequencing. microPIPE was developed to automate high-quality complete bacterial genome assembly using Oxford Nanopore Sequencing in combination with Illumina sequencing.

A genome assembly correction and scaffolding pipeline using long reads.

A quality assessment tool for genome assemblies and gene structure annotations. GenomeQC generates descriptive summaries with intuitive graphics for genome assembly and structural annotations. It also benchmarks user supplied assemblies and annotations against the publicly available reference genomes of their choice. It is optimized for small and medium sized genomes (<2.5 Gb) and has pre-computed results for several maize genomes.

Structural variant detection from haploid and diploid genome assemblies. SVIM-asm - Structural variant identification method (Assembly edition). SVIM-asm (pronounced SWIM-assem) is a structural variant caller for haploid or diploid genome-genome alignments. It analyzes a given sorted BAM file (preferably from minimap2) and detects five different variant classes between the query assembly and the reference: deletions, insertions, tandem and interspersed duplications and inversions.