BOL: Related items

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

Learn Genetics Online

Rahul Agarwal — Wed, 09 Apr 2014 19:12:42 -0500

Great source to learn genetics and other relevant stuffs online.

Address of the bookmark: http://learn.genetics.utah.edu/

BreakSeq2

Jitendra Narayan — Mon, 29 Feb 2016 17:45:38 -0600

Ultrafast and accurate nucleotide-resolution analysis of structural variants

More at http://bioinform.github.io/breakseq2/

Download BreakSeq2

Latest version: https://github.com/bioinform/breakseq2/archive/2.2.tar.gz

For other versions, see "releases". https://github.com/bioinform/breakseq2/releases

Address of the bookmark: http://bioinform.github.io/breakseq2/

Maq: Mapping and Assembly with Quality

Jit — Tue, 22 Nov 2016 04:51:39 -0600

Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/. Maq is previously known as mapass2.

Run Maq Now

Follow these steps to try Maq. All you need is a reference sequence file in the FASTA format.

Prepare a reference sequence (ref.fasta). Better a bacterial genome.
Download maq, maq-data and maqview at the download page.
Copy maq, maq.pl and maq_eval.pl to the $PATH or to the same directory.
Simulate diploid reference and read sequences, map reads, call variants and evaluate the results in one go:
```
maq.pl demo ref.fasta calib-30.dat
```
where calib-30.dat is contained in maq-data.

View the alignment:

cd maqdemo/easyrun;
maqindex -i -c consensus.cns all.map;
maqview -c consensus.cns all.map

Even for advanced maq users, running `maq.pl demo' is recommended. You may find something helpful.

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

Dynamic Programming Alignment

Thu, 22 Aug 2013 09:38:28 -0500

lecture 9, Chem. C100, Spring 2013, UCLA

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/

YAHA

Jit — Fri, 20 Jan 2017 05:38:05 -0600

YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints.

Availability: YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from http://faculty.virginia.edu/irahall/YAHA.

Contact:

http://genome.wustl.edu/people/groups/detail/hall-lab/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463118/

GenomeComp

Jit — Fri, 17 Feb 2017 08:38:32 -0600

GenomeComp is a tool for summarizing, parsing and visualizing the genome wide sequence comparison results derived from voluminous BLAST textual output, so as to locate the rearrangements, insertions or deletions of genome segments between species or strains.

It can be easily used to compare, parsing and visualize large genomic sequences, especially closely related genomes such as inter-species or inter-strains. In addition, it can also show other sequence features like repeat sequence distributions in one whole-genome DNA sequence by comparing the genome to itself.

It is a stand-alone graphical user interface (GUI) program which runs on Linux, Unix, Mac OS X (tested on version 10.2.4 only) and Microsoft Windows platforms and is written in Perl/Tk.

Address of the bookmark: http://www.mgc.ac.cn/GenomeComp/

Cgaln

Jit — Wed, 22 Feb 2017 05:14:15 -0600

Cgaln (Coarse grained alignment) is a program designed to align a pair of whole genomic sequences of not only bacteria but also entire chromosomes of vertebrates on a nominal desktop computer. Cgaln performs an alignment job in two steps, at the block level and then at the nucleotide level. The former "coarse-grained" alignment can explore genomic rearrangements and reduce the regions to be analyzed in the next step. The latter is devoted to detailed alignment within the limited regions found in the first stage. The output of Cgaln is 'glocal' in the sense that rearrangements are taken into consideration while each alignable region is extended as long as possible. Thus, Cgaln is not only fast and memory-efficient, but also can filter noisy outputs without missing the most important homologous segment pairs.

http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/cgaln/

Address of the bookmark: http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/cgaln/