BOL: Related items

Quota synteny alignment

Jit — Mon, 31 Jul 2017 04:11:57 -0500

Typically in comparative genomics, we can identify anchors, chain them into syntenic blocks and interpret these blocks as derived from a common descent. However, when comparing two genomes undergone ancient genome duplications (plant genomes in particular), we have large number of blocks that are not orthologous, but are paralogous. This has forced us sometimes to use ad-hoc rules to screen these blocks. So the question is: given the expected depth (quota) along both x- and y-axis, select a subset of the anchors with maximized total score.

Address of the bookmark: https://github.com/tanghaibao/quota-alignment

Mugsy: multiple whole genome alignment tool

Jit — Fri, 08 Dec 2017 17:41:14 -0600

Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.

To cite Mugsy, use:

Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes.Bioinformatics 2011 27(3):334-4

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

assemblytics: delta file to analyze alignments of an assembly to another assembly or a reference genome

Jit — Thu, 14 Jun 2018 07:31:00 -0500

Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip the delta file to speed up upload (usually 2-4X faster) $ gzip OUT.delta Then use the OUT.delta.gz file for upload. Upload the .delta or delta.gz file (view example) to Assemblytics Important: Use only contigs rather than scaffolds from the assembly. This will prevent false positives when the number of Ns in the scaffolded sequence does not match perfectly to the distance in the reference. The unique sequence length required represents an anchor for determining if a sequence is unique enough to safely call variants from, which is an alternative to the mapping quality filter for read alignment. http://assemblytics.com/

Address of the bookmark: http://assemblytics.com/

The wavefront alignment (WFA) algorithm

BioStar — Sun, 28 Jun 2020 10:17:50 -0500

The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of
homologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns), proportional to the read length n and the alignment score s, using O(s^2) memory. Moreover, the WFA exhibits simple data dependencies that can be easily vectorized, even by the automatic features of modern compilers, for different architectures, without the need to adapt the code.

Address of the bookmark: https://github.com/smarco/WFA

A web-based tool for sequence alignment statistics and innovative visualization

BioStar — Thu, 04 Apr 2024 01:44:50 -0500

AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/

Alvis: a tool for contig and read ALignment VISualisation and chimera detection

LEGE — Wed, 08 May 2024 07:02:55 -0500

Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04056-0

Address of the bookmark: https://github.com/SR-Martin/alvis

SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs

Neel — Sun, 20 Dec 2020 01:39:54 -0600

The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short (Illumina) and long (ONT and PacBio) reads. Described by Alser et al. (preliminary version at https://arxiv.org/abs/1910.09020).

Address of the bookmark: https://github.com/CMU-SAFARI/SneakySnake

FRODOCK 2.0: fast protein–protein docking server

Neel — Wed, 17 Oct 2018 04:31:30 -0500

frodock: a user-friendly protein–protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select protein–protein models and interactively screen them against experimental distance constraints. The competitive success rates and efficiency achieved allow the retrieval of reliable potential protein–protein binding conformations that can be further refined with more computationally demanding strategies.

Address of the bookmark: http://frodock.chaconlab.org/

SeQuiLa-cov: A fast and scalable library for depth of coverage calculations

Jit — Sun, 15 Dec 2019 10:19:35 -0600

The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary information on benchmarking procedure as well as test data are publicly accessible at the project documentation site http://biodatageeks.org/sequila/benchmarking/benchmarking.html#depth-of-coverage. An archival copy of the code and supporting data is also available via the GigaScience database GigaDB

• Project name: SeQuiLa-cov

• Project home page: http://biodatageeks.org/sequila/

• Source code repository: https://github.com/ZSI-Bio/bdg-sequila

• Operating system: Platform independent

• Programming language: Scala

• Other requirements: Docker

• License: Apache License 2.0

Address of the bookmark: https://academic.oup.com/gigascience/article/8/8/giz094/5543653

PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index

Rahul Nayak — Thu, 21 Apr 2022 05:41:39 -0500

PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish index. PuffAligner is able to produce highly sensitive alignments, similar to those of Bowtie2, but much more quickly. While exhibiting similar speed to the ultrafast STAR aligner, PuffAligner requires considerably less memory to construct its index and align reads. PuffAligner strikes a desirable balance with respect to the time, space and accuracy tradeoffs made by different alignment tools and provides a promising foundation on which to test new alignment ideas over large collections of sequences.

Address of the bookmark: https://github.com/COMBINE-lab/pufferfish/tree/cigar-strings