BOL: Related items

MutaBind

Jit — Mon, 06 Jun 2016 13:34:09 -0500

MutaBind is a new computational method and server created through NCBI research efforts that maps mutations on a protein structural complex, calculates changes in binding affinity, identifies deleterious mutations and produces a downloadable mutant structural model. http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

MutaBind guides you through this process, step by step, starting with selecting a protein complex and inputting PDB code or uploading PDB files. You can also retrieve results with a job ID number, view help documents, and review the MutaBind method and references.

More at http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

Latest paper on comparison of mapping tools

Rahul Agarwal — Tue, 03 Sep 2013 18:00:38 -0500

A. Hatem, D. Bozdag, A. E. Toland, U. V. Catalyurek "Benchmarking short sequence mapping tools" BMC Bioinformatics, 14(1):184, 2013.

http://bmi.osu.edu/hpc/software/benchmark/

http://bmi.osu.edu/hpc/software/pmap/pmap.html

Other similiar papers:

http://online.liebertpub.com/doi/pdf/10.1089/cmb.2012.0022

http://bioinformatics.oxfordjournals.org/content/28/24/3169

Some new Mapping tool links:

GSNAP

http://research-pub.gene.com/gmap/

RMAP

http://rulai.cshl.edu/rmap/

mrsFAST

http://mrsfast.sourceforge.net/Home

http://sourceforge.net/projects/mrsfast/files/mrsfast-ultra-3.1.0/

BFAST

http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page

SHRiMP (for AB SOLiD color-space reads)

http://compbio.cs.toronto.edu/shrimp/

RazerA 3

http://www.seqan.de/projects/razers/

Address of the bookmark: http://www.biomedcentral.com/1471-2105/14/184

SNPGenie

Jit — Thu, 30 Mar 2017 17:38:02 -0500

SNPGenie is a Perl script for estimating evolutionary parameters, mainly from pooled next-generation sequencing (NGS) single-nucleotide polymorphism (SNP) variant data. SNP reports (acceptable in a variety of formats) much each correspond to a single population, with variants called relative to a single reference sequence (one sequence in one FASTA file). Just run the main script, snpgenie.pl, in a directory containing the necessary input files, and we take care of the rest! For the earlier version, see Hughes Lab Bioinformatics Resource.

Address of the bookmark: https://github.com/hugheslab/snpgenie

Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search

Jit — Tue, 28 Jan 2020 03:34:23 -0600

Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only

Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can be unpractical for large error prone genomes which makes the assembly process produce an excessive number of false positive cycles. Our solution is to search the graph in multicores shared memory parallel mode using graph decomposition then use filtering method to generate good quality SNPs.

https://arxiv.org/abs/1809.06700

https://github.com/redayounsi/2KP2P

/2kp2omp/bin/main_2kp2_K63_C2 -i fastq_files.txt -o fungus_bub.fasta -r stat_fungus.txt -c cov_fungus_hash.txt -k 63 -h 20 -b 100 -g 600 -l 100 -f 16 -t 5.0 -x 1 -v 0 -p 1 -y 1 -u 1

Address of the bookmark: https://github.com/redayounsi/2KP2P

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

geck: trio-based comparative benchmarking of variant calls

Jit — Sun, 19 May 2019 20:54:12 -0500

Determine the accuracy of our model by comparing the precision and recall of GATK Unified Genotyper and Haplotype Caller on the high-confidence SNPs of the NIST Ashkenazim trio and the two independent Platinum Genome trios. We show that our method is able to estimate differential precision and recall between the two pipelines with 10−3uncertainty.

Address of the bookmark: https://github.com/sbg/geck

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

Fastq format

Jit — Wed, 03 May 2017 04:23:32 -0500

FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.

It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA sequence and its quality data, but has recently become the de facto standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer.^[1]

Address of the bookmark: https://en.wikipedia.org/wiki/FASTQ_format

Tigers genome sequenced

Rahul Agarwal — Tue, 17 Sep 2013 16:48:24 -0500

Fifteen scientists led by Dr Jong Bhak of Genome Research Foundation, South Korea, decoded as many as 3 billion nucleotides (organic molecules that form the basic building blocks of nucleic acids, such as DNA). They identified 20,000 genes related to various functions of the tiger.

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html

Opera: An optimal genome scaffolding program

Jit — Mon, 27 Nov 2017 10:18:20 -0600

Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

An updated version called OPERA-LG has been re-engineered with features for the assembly of large and complex genomes.

Song Gao, Denis Bertrand, Burton K. H. Chia and Niranjan Nagarajan. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biology, May 2016, doi: 10.1186/s13059-016-0951-y.

Song Gao, Wing-Kin Sung, Niranjan Nagarajan. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb.2011.0170.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0951-y

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