BOL: Related items

Hagfish - assess an assembly through creative use of coverage plots

Abhi — Fri, 20 May 2016 19:08:17 -0500

Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or identification of structural variation in a genome re-sequencing experiment.

Hagfish requires a reference sequence and a paired end re-sequencing data set. Hagfish has more power the larger the insert size of the paired end library is.

Quick links: Installation,Operation, Read mappers, Hagfish scripts, Hagfish plots

Address of the bookmark: https://github.com/mfiers/hagfish

SeqMule: Automated human exome/genome variants detection

Abhimanyu Singh — Tue, 07 Mar 2017 10:12:36 -0600

SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study.

Address of the bookmark: http://seqmule.openbioinformatics.org/en/latest/

Ensembl comparative genomics resources

Jitendra Narayan — Sun, 28 Feb 2016 17:10:20 -0600

The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.

Database URL: http://www.ensembl.org.

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/

Ensembl 27

Jit — Tue, 16 Jun 2015 16:10:36 -0500

What is new?

Expansion of Protists and Fungi with hundreds of annotated genomes
Variation data for bread wheat, rice, Aedes aegypti, and Ixodes scapularis
Whole genome alignments for O. longistaminata and T. cacao
Non-coding RNA gene models in Bacteria
New assembly of tomato (version 2.50)
Full support for UCSC Track Hub format for hosting your own data in Ensembl

More at http://www.ensembl.info/blog/2015/06/16/ensembl-genomes-release-27-is-out/

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

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

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

vt: a variant tool set that discovers short variants from Next Generation Sequencing data.

Jit — Tue, 28 Jan 2020 03:44:43 -0600

vt is a variant tool set that discovers short variants from Next Generation Sequencing data.

https://genome.sph.umich.edu/wiki/Vt

https://github.com/atks/vt

Address of the bookmark: https://genome.sph.umich.edu/wiki/Vt

truvari: Structural variant comparison tool for VCFs

Jit — Tue, 30 Jun 2020 21:30:44 -0500

Structural variant comparison tool for VCFs

Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure.

Spiral Genetics

Motivation

Address of the bookmark: https://github.com/spiralgenetics/truvari

Minda: a tool for evaluating structural variant (SV) callers

LEGE — Sun, 31 Mar 2024 02:43:50 -0500

Minda is a tool for evaluating structural variant (SV) callers that

standardizes VCF records for compatibility with both germline and somatic SV callers,
benchmarks against a single VCF input file, or
benchmarks against an ensemble call set created from multiple VCF input files.

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