BOL: Related items

MMseqs2.0: ultra fast and sensitive protein search and clustering suite

Jit — Thu, 22 Mar 2018 10:40:51 -0500

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

The MMseqs2 user guide is available as Github Wiki or as PDF file (Thanks to pandoc!)

Please cite: Steinegger M and Soeding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, doi: 10.1038/nbt.3988 (2017).

Address of the bookmark: https://github.com/soedinglab/MMseqs2

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Manisha Mishra — Mon, 18 Jan 2021 10:47:56 -0600

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

Address of the bookmark: https://github.com/soedinglab/MMseqs2

CovCal: Coverage / Read Count Calculator

Jit — Wed, 15 Jun 2016 18:08:13 -0500

Coverage / Read Count Calculator

Calculate how much sequencing you need to hit a target depth of coverage (or vice versa).

Instructions: set the read length/configuration and genome size, then select what you want to calculate.

Written by Stephen Turner, based on the Lander-Waterman formula, inspired by a similar calculator written by James Hadfield. Coverage is calculated as C=LN/G and reads as N=CG/L where C = Coverage (X),L = Read length (bp), G = Haploid genome size (bp), and N = Number of reads. Source code on GitHub.

Address of the bookmark: http://apps.bioconnector.virginia.edu/covcalc/

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Abhimanyu Singh — Tue, 23 May 2017 05:28:56 -0500

SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1344-7

Address of the bookmark: http://ufmg-simba.sourceforge.net/

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

CNIDARIA: fast, reference-free phylogenomic clustering

Shruti Paniwala — Thu, 16 Jun 2016 17:55:17 -0500

Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances.

Results: We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on ge-nome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100% accuracy at supra-species level and 78% accuracy for species level.

Availability and Implementation: Cnidaria is written in C++ and Python and is available at http://www.ab.wur.nl/cnidaria.

Contact: Saulo Aflitos - sauloal@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Address of the bookmark: https://github.com/sauloal/cnidaria/wiki

CLARK: Fast, accurate and versatile sequence classification system

Jit — Sat, 15 Feb 2020 01:49:01 -0600

CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to known bacterial genomes, and (2) the assignment of BAC clones and transcript to chromosome arms/centromeres (in the absence of a finished assembly for the reference genome), CLARK outperforms in classification speed and precision the best state-of-the-art methods.

http://clark.cs.ucr.edu/Spaced/

Address of the bookmark: http://clark.cs.ucr.edu/Spaced/

MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)

Jit — Tue, 12 Dec 2017 17:23:31 -0600

MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but rather estimates a k-mer based Jaccard similarity using a combination of Winnowing and MinHash. This is then converted to an estimate of sequence identity using the Mash distance. An appropriate k-mer sampling rate is automatically determined given minimum local alignment length and identity thresholds. The efficiency of the algorithm improves as both of these thresholds are increased.

Address of the bookmark: https://github.com/marbl/MashMap

Kalign: fast multiple sequence alignment program for biological sequences.

BioStar — Fri, 01 Nov 2019 00:20:41 -0500

Kalign is a fast multiple sequence alignment program for biological sequences.

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Address of the bookmark: https://github.com/TimoLassmann/kalign

RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes

Rahul Nayak — Fri, 01 May 2020 03:00:40 -0500

RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step.

Address of the bookmark: https://github.com/AppliedBioinformatics/RefKA