BOL: Related items

Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data

Shruti Paniwala — Thu, 25 Oct 2018 06:14:55 -0500

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole-genome, exon-capture, and targeted capture data, it has been run on very large datasets as part of the Thousand Genomes and WGS500 projects, and is being used in clinical sequencing trials in the Mainstreaming Cancer Genetics programme.

Tutorial https://github.com/andyrimmer/Platypus/blob/master/misc/README.txt

Address of the bookmark: http://www.well.ox.ac.uk/platypus

Classification of SARS-CoV2 Variant !

Jit — Fri, 26 Nov 2021 12:53:12 -0600

The scientists established some guidelines for determining whether a variant is a legitimate branch of an existing lineage:

The variant should be transmitted from its original location to another "geographically distinct population"—say, another country or a province of a large and populous country.
It should differ from its ancestor by at least one nucleotide.
At least 95% of its genetic code should have been sequenced at least five times from different samples.

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/

Kevler: Reference-free variant discovery in large eukaryotic genomes

Jit — Tue, 28 Jan 2020 03:21:53 -0600

Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs), insertion/deletion variants (indels), and structural variants (SVs) simultaneously with a single simple model.

More at https://kevlar.readthedocs.io/en/latest/

https://www.cell.com/iscience/pdf/S2589-0042(19)30259-7.pdf

Address of the bookmark: https://github.com/kevlar-dev/kevlar

Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Jit — Thu, 28 May 2020 21:57:03 -0500

Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a region, Inversions of a region, or Translocations between two regions in the genome.

Parliament2 runs a combination of tools to generate structural variant calls on whole-genome sequencing data. It can run the following callers: Breakdancer, Breakseq2, CNVnator, Delly2, Manta, and Lumpy. Because of synergies in how the programs use computational resources, these are all run in parallel. Parliament2 will produce the outputs of each of the tools for subsequent investigation.

Address of the bookmark: https://github.com/dnanexus/parliament2

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

Corona Virus Genome and Data Download !

Abhi — Sun, 12 Dec 2021 23:34:54 -0600

Genes and its related metadata could be found on https://www.ncbi.nlm.nih.gov/datasets/coronavirus/genomes/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/datasets/coronavirus/genomes/

Which are the best statistical programming languages to study for a bioinformatician?

Jitendra Narayan — Wed, 10 Jul 2013 14:35:34 -0500

In Bio-informatics based genome sequencing and predicting metabolic pathways research jobs I used Matlab, SAS, SPSS, R and several Bioconductor packages. Matlab had a lot of powerful tools and was easy to use, whereas SPSS is for non-programmers and R need programming skills. I am wondering what other people think is best? or there might not be one specific language but a few that lend themselves best to Bio-informatics work that is math heavy and deals with a large amount of data.

Smyth Lab

Sun, 14 Jul 2013 12:26:18 -0500

Statistical functional genomics in experimental medicine
The genome projects and the accelerated development of high-throughput genomic technologies such as microarrays have revolutionised biology. Making the most of this revolution requires the marriage of researchers from mathematical and biological backgrounds.

Research Area:
Linear models for microarray data
Digital gene expression technologies
Detection of molecular pathways
Bioinformatics resources for medical research

Link @ http://www.wehi.edu.au/faculty_members/professor_gordon_smyth/

ISCB-Asia 2013 Translational Bioinformatics Conference

Thu, 08 Aug 2013 06:31:32 -0500

ISCB-Asia 2013
Translational Bioinformatics Conference
Seoul, Korea
October 2 - 4, 2013

For more information visit: http://www.snubi.org/TBC2013/