BOL: Related items

DAVI: Deep learning-based tool for alignment and single nucleotide variant identification

Jit — Tue, 16 Mar 2021 05:41:33 -0500

DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools used for bench-marking. We further demonstrate that while existing tools are based on data generated from a specific sequencing technology, the models proposed in DAVI are generic and can be used across different NGS technologies as well as across different species

https://iopscience.iop.org/article/10.1088/2632-2153/ab7e19/pdf

Address of the bookmark: https://github.com/gguptaiitd/NEAT

Ensembl Variation - Calculated variant consequences

Jit — Sun, 09 Sep 2018 19:17:37 -0500

For each variant that is mapped to the reference genome, we identify all overlapping Ensembl transcripts. We then use a rule-based approach to predict the effects that each allele of the variant may have on each transcript. The set of consequence terms, defined by the Sequence Ontology (SO), that can be currently assigned to each combination of an allele and a transcript is shown in the table below. Note that each allele of each variant may have a different effect in different transcripts.

Address of the bookmark: https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html

Snippy: Rapid haploid variant calling and core SNP phylogeny

Neel — Sat, 11 Aug 2018 11:06:56 -0500

Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and generate a core SNP alignment (and ultimately a phylogenomic tree).

snippy --cpus 16 --outdir mysnps --ref Listeria.gbk --R1 FDA_R1.fastq.gz --R2 FDA_R2.fastq.gz

Address of the bookmark: https://github.com/tseemann/snippy

AlfaPang: alignment free algorithm for pangenome graph construction

BioStar — Thu, 28 Aug 2025 02:56:35 -0500

AlfaPang constructs variation graphs, leveraging its alignment-free and reference-free approach, based solely on intrinsic sequence properties. This design allows AlfaPang's runtime and memory usage to scale linearly with the size of input sequences, enabling it to handle significantly larger genome sets compared to other methods.

Address of the bookmark: https://github.com/AdamCicherski/AlfaPang

AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing

BioStar — Fri, 22 Dec 2017 00:31:06 -0600

AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to conventional public pipelines and ∼48% to the in-house commercial solution, with a minimal loss of sensitivity

The program with a detailed manual is available at https://sourceforge.net/projects/airvf/

Address of the bookmark: https://sourceforge.net/projects/airvf/

Best Practices for Variant Calling with the GATK

biogeek — Sat, 22 Feb 2020 03:07:31 -0600

The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version 3.3.

Genome Analysis Toolkit

03/19/15	Introduction to High-Throughput Sequencing data formats and methods	Joel Thibault	PDF	Video
03/19/15	Introduction to the GATK	Geraldine Van der Auwera	PDF	Video
03/19/15	Mapping, processing, and duplicate marking with Picard tools	Matt Sooknah	PDF	Video
03/19/15	Mapping and processing RNAseq	Ami Levy-Moonshine	PDF	Video
03/19/15	Indel realignment	Mark Fleharty	PDF	Video
03/19/15	Base quality score recalibration	David Roazen	PDF	Video
03/19/15	Introduction to variant discovery: calling cohorts	Louis Bergelson	PDF	Video
03/19/15	Variant calling and joint genotyping	Sheila Chandran	PDF	Video
03/19/15	Variant quality score recalibration	Bertrand Haas	PDF	Video
03/19/15	Introduction to working with variants	Yossi Farjoun	PDF	Video
03/19/15	Genotype refinement	Laura Gauthier	PDF	Video
03/19/15	Annotation and variant evaluation	David Benjamin	PDF	Video

Address of the bookmark: https://www.broadinstitute.org/partnerships/education/broade/best-practices-variant-calling-gatk-1

GFAffix : Identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.

BioStar — Thu, 28 Aug 2025 03:11:25 -0500

GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.

Address of the bookmark: https://github.com/codialab/GFAffix

Calling variants in non-diploid systems

Neel — Sat, 26 Jun 2021 15:37:49 -0500

The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA although the same approaches will work equally good on viral and bacterial genomes (Rebolledo-Jaramillo et al. 2014, Li et al. 2015).

Address of the bookmark: https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html

Variant Calling Resequencing-Based Genome Inference

Abhi — Wed, 31 Jul 2024 02:02:24 -0500

Variant Calling - Resequencing-Based Genome Inference

Erik Garrison
University of Tennessee Health Science Center
Workshop on Genomics - Český Krumlov
January 12, 2024

https://evomics.org/wp-content/uploads/2024/01/Variant-calling-Workshop-on-Genomics-2024-Cesky-Krumlov.pdf

Address of the bookmark: https://evomics.org/wp-content/uploads/2024/01/Variant-calling-Workshop-on-Genomics-2024-Cesky-Krumlov.pdf

High Density Sheep SNP Genotyping Chip released!!!

Rahul Agarwal — Tue, 03 Sep 2013 13:58:04 -0500

If you are working on Sheep genomics then there is a good news for you. FarmIQ in conjunction with Illumina and the International Sheep Genomics Consortium (ISGC) are today announcing completion of the “Ovine Infinium® HD SNP BeadChip”, a high definition SNP chip for ship genome. The OvineSNP50 BeadChip features over 54,241 evenly spaced probes that target SNPs, offering more than sufficient SNP density for genome-wide association studies and other applications such as genome-wide selection, determination of genetic merit, identification of quantitative trait loci, and comparative genetic studies.

The BeadChip was developed in collaboration with leading ovine researchers from AgResearch, Baylor UCSC, CSIRO, and the USDA as part of the International Sheep Genomics Consortium. It features over 54,241 evenly spaced probes that target single nucleotide polymorphisms (SNPs). More than 18,000 of these markers were discovered through sequencing reduced representation libraries with the Illumina Genome Analyzer IIx. A set of 600 SNPs were identified by BAC end sequencing and validated with Illumina GoldenGate Genotyping Assays over 403 animals from 23 breeds. The remaining SNPs were derived from the draft ovine genome.