BOL: Related items

SvABA: Genome-wide detection of structural variants and indels by local assembly

Abhimanyu Singh — Mon, 21 Jan 2019 17:58:56 -0600

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (with some small overlap) for every region in the genome. The default is to use only clipped, discordant, unmapped and indel reads, although this can be customized to any set of reads at the command line using VariantBam rules. These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support.

Address of the bookmark: https://github.com/walaj/svaba

vsFilt: A tool to improve virtual screening by structural filtration of docking poses

Neel — Wed, 25 Nov 2020 02:39:16 -0600

The vsFilt is the first open application for post-docking structural filtration, available as a web-server. The new tool is easy to use and configure to detect a wide range of interaction types that are known to be involved in molecular recognition, including hydrogen and halogen bonds, ionic interactions, hydrophobic contacts, π-stacking, and cation-π interactions. The web-server can process large libraries of up to 150’000 docked ligand poses. The results are web-based and can be operated on-line using the built-in HTML5 interactive analysis tools, or can be downloaded for a local use. The vsFilt is freely available on-line, no login required.

Address of the bookmark: https://biokinet.belozersky.msu.ru/vsfilt

Severus: a somatic structural variation (SV) caller for long reads

LEGE — Sun, 31 Mar 2024 02:41:27 -0500

Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT). It is designed for matching tumor/normal analysis, supports multiple tumor samples, and produces accurate and complete somatic and germline calls. Severus takes advantage of long-read phasing and uses the breakpoint graph framework to model complex chromosomal rearrangements.

If you use Severus, please cite https://www.medrxiv.org/content/10.1101/2024.03.22.24304756v1

Address of the bookmark: https://github.com/KolmogorovLab/Severus

SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator

Jit — Sat, 04 Jul 2020 05:52:34 -0500

SVEngine (Structural Variants Engine)

SVEngine is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios.
SVEngine takes as input reference contigs in FASTA files, variant meta distribution as specified in META files (see Manual) or specific variant information as specified in VAR files (see Manual) and NEWICK files for specifying clonal phylogenetic trees in cancer.
SVEngine outpus alterred contigs in FASTA files, spiked-in variants in VAR files (see Manual), simulated short read in FASTQ files and aligned short reads in BAM files.

Address of the bookmark: https://bitbucket.org/charade/svengine/src/master/

SATSUMA : Highly sensitive whole-genome synteny alignments.

Jit — Fri, 13 May 2016 05:25:26 -0500

Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does not require any pre-processing, such as repeat masking, since it will automatically detect ambiguous mappings.

Satsuma has parallelization built-in and is designed to run on multi-core architectures. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days on 24 CPUs.

You can find the manual here.
Download the latest source code from here.
Stable versions can also be downloaded from the Broad Institute's web site.

An incomplete list of questions and answers (yes, these have really been asked by our users! Please feel free to add your own by e-mailing us) is here.

If you use Satsuma in your research, please cite:
Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51.

Tutorial at http://evomics.org/learning/genomics/satsuma/

Address of the bookmark: http://satsuma.sourceforge.net/

Spines

Jit — Mon, 28 Nov 2016 05:33:26 -0600

Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets for various analyses. It also features three sequence alignment packages: Satsuma, a highly parallelized program for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with large gaps.

Access Spines here.

Address of the bookmark: https://www.broadinstitute.org/genome-sequencing-and-analysis/spines

maf2synteny

Abhimanyu Singh — Thu, 18 May 2017 05:31:30 -0500

A tool for converting for recovering synteny blocks from multiple alignment (in MAF fromat)

This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]

Address of the bookmark: https://github.com/fenderglass/maf2synteny

Synima: Synteny Imaging tool

Jit — Sun, 10 Dec 2017 17:03:48 -0600

Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Address of the bookmark: https://github.com/rhysf/Synima

Apollo: a sequence annotation editor

Abhimanyu Singh — Tue, 27 Aug 2019 08:08:47 -0500

The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them

Address of the bookmark: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2002-3-12-research0082

Sibelia: A comparative genomics tool

BioStar — Sat, 22 Aug 2020 02:49:00 -0500

Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.

Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes.

More at http://bioinf.spbau.ru/sibelia

Sibelia docs http://gensoft.pasteur.fr/docs/Sibelia/3.0.7/SIBELIA.md

Address of the bookmark: https://github.com/bioinf/Sibelia