Find open-source science resources

JCVI is a versatile toolkit for comparative genomics analysis. It is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

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.

Circlator is a tool to circularize genome assemblies. It will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.

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.

Screen a bacterial assembly (contigs/CDS or proteins) for nucleotide or protein sequences. Pipeline that screens for presence of genes of interest (GOI) in bacterial assemblies. Generates multiple CSVs and plots that describe which genes are present and how variable their sequence is. Can use DNA or protein query sequences (GOIs) and DNA contigs/fastas or protein fastas as database (db) to search in.

agtools is a Python framework for manipulating assembly graphs, facilitating downstream analyses in metagenomics. It provides command-line and Python interfaces to parse, convert, filter, and analyze graph formats like GFA.

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.

WGA-LP is a pipeline for whole genome assembly that simplifies the usage of different tools and helps the user in evaluating his results.

Structural Variants Assessment Based on Haplotype-resolved Assemblies.

Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line.

A system for managing local collections biological sequences. Python package for writing and reading a local collection of biological sequences. The repository is non-redundant, compressed, and journalled, making it efficient to store and transfer multiple snapshots. A "fully-qualified" identifier includes a namespace to disambiguate accessions (e.g., "1" in GRCh37 and GRCh38). If the namespace is provided, seqrepo uses it as-is. If the namespace is not provided and the unqualified identifier refers to a unique sequence, it is returned; otherwise, ambiguous identifiers will raise an error.

SearcHPV detects HPV fusion sites on both human genome and HPV genome. SearcHPV is able to provide locally assembled contigs for each integration events. It will report at least one and at most two contigs for each integration sites. The two contigs will provide information captured for left and right sides of the event. SearcHPV is a novel approach to identify and assemble human papillomavirus-host genomic integration events in cancer.

A Massively Parallel Method for Accelerating Protein Structure Reconstruction from Internal Coordinates.

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.

BubbleGun is a tool for detecting Bubbles and Superbubble in De-bruijn graphs. BubbleGun outputs runs of bubbles and superbubbles we call bubble chains.

Design and assembly of DNA molecules using multi-objective optimisation | A DNA design and assembly method based on multi-objective optimization | MOODA: Multi-Objective Optimization for DNA sequence Design and Assembly | A manufacturing-aware sequence optimizer | Write a MOODA configuration file. A .yaml file defining operators, objective functions, assemblies strategy and their parameters, this is how a MOODA configuration file looks like:

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.

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.