Open-source tools

Genomics information and bioinformatics tools developed in the frame of research projects are made publicly available by IGA.

You can explore sequenced genomes using blast search pages and genome browsers for grapevine, peach and poplar. IGA genome browsers contain basic tracks available from collaborative information systems and annotation tracks that have been computed at IGA.

Bioinformatic tools produced by IGA are "open source". Have a look at available software tools.

ERNE

ERNE (Extended Randomized Numerical alignEr) is a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE comprises ERNE-MAP (align short DNA or RNA reads against a genome), ERNE-DMAP (distributed version of the aligner), ERNE- BS5 (align short reads treated with bisulfite against a genome), ERNE-FILTER (a quality trimming and contamination filter for de novo assembly that can also be used for alignments), and ERNE-VISUAL (graphical user interface).

ERNE is an open source project. The source code and executables for GNU/Linux, Windows, and OSX are available on SourceForge.

COREFINDER

COREFINDER is a software for sorting out a core collection from a large database of individual molecular profiles. Read the tutorial or download the software

SmartFinder

SMaRTFinder is a command line tool to search biosequences for structured motifs (or structured models); that is lists of patterns separated by distance intervals. It reads a sequence in FASTA format and a structured model specification, either from a file or from the standard input, then searches for exact/approximate occurrences of the structured model (in one or both strands, if the sequence is DNA) and outputs a file in GFF format.

LadderFinder

LadderFinder is a program designed to solve a problem in DNA genotyping. It helps in the construction of allelic ladders that drive the sizing and binning of SSR fragments produced by PCR. The algorithm scans a spreadsheet containing a database of individual profiles and finds a minimum set of individuals that covers the maximum number of alleles represented in the database, with all alleles represented only once. The last constraint is imposed to make homogeneous the ladder peaks in the pherograms. Given such a constraint, the best solution may not include all alleles.

matchfinder

Matchfinder computes a maximal matching of a graph. A matching of a graph G is a set of pairwise non-adjacent edges of G. A maximal matching for G is a matching of maximum cardinality with respect to G. Notice that there can be many different maximal matchings for a single graph. For instance, the graph G=( V={1, 2, 3}, E={(1,2), (2,3)} has two maximal matchings: M={(1,2)} and M={(2,3)}.

Genome Assemblies Merger

GAM is a free parallel software tool to integrate two different assemblies and improve the overall quality of the genome sequences by merging them. It discovers and aligns similar sequences by using the positions of placed reads. An ordered sequence of reads contiguous on the same contig is called a frame. When the same frame is shared by both original assemblies, GAM dubs it block.

GAM deduces block orders from assembly read orders and, by using them, builds a graph of assemblies whose nodes represent blocks and whose edges represents block orders. Since cycles in the graph of assemblies denote conflicting block order in assemblies, GAM avoids merging sequences containing blocks belonging to them.

χ-SCAN

χ-SCAN is a software package to identify mosaic (and germline) structural variants (SVs) using whole-genome resequencing data. χ-scan computes deviations from the expected allele frequency in a population of cells, using counts of aligned reads covering heterozygous SNP sites, to detect signals of reduction of heterozygosity (ROH), which can be caused (among others) by events of deletion, CNV, or chromosomal replacement. χ- SCAN offers a number of statistical tests to assess the significance of the detected ROHs.

Marroni et al (2017) Reduction of heterozygosity (ROH) as a method to detect mosaic structural variation. Plant Biotechnology Journal doi: 10.1111/pbi.12691