BOL: Related items

RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler

LEGE — Thu, 09 Jul 2020 03:13:06 -0500

RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types:

single-end/paired-end bulk RNA-seq (strand-specific/agnostic)
paired-end single-cell RNA-seq (strand-specific/agnostic)
nanopore RNA-seq (PCR cDNA/direct cDNA/direct RNA)

Written by Ka Ming Nip ✉️

Address of the bookmark: https://github.com/bcgsc/RNA-Bloom

Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map

Jit — Wed, 11 Mar 2020 01:12:06 -0500

A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg)

Link to working demo: https://vgteam.github.io/sequenceTubeMap/

Address of the bookmark: https://github.com/vgteam/sequenceTubeMap

Sequence Viewer: Download Transcripts, Exons and Proteins

Mon, 15 Sep 2014 17:30:36 -0500

How to download FASTA sequence for certain gene features while in the NCBI's Sequence Viewer. Sequence Viewer homepage: www.ncbi.nlm.nih.gov/projects/sviewer/ Sequence Viewer playlist: https://www.youtube.com/playlist?list=PL76D7EE6A6A8AC1C3

STELLAR: fast and exact local alignments

Neel — Wed, 29 Aug 2018 16:00:46 -0500

STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar.

Address of the bookmark: http://www.seqan.de/apps/stellar/

FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

Jit — Fri, 08 Dec 2017 14:41:08 -0600

Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a greedy way taking the symbols from the given pair of sequences (protein or nucleotide) and results in an optimal alignment faster than conventional dymanic programming techniques. It is also better than the heuristic methods with respect to alignment quality.

Address of the bookmark: http://www.isical.ac.in/~bioinfo_miu/FOGSAA.htm

ANItools web: a web tool for fast genome comparison within multiple bacterial strains

Jit — Wed, 14 Nov 2018 04:34:23 -0600

ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you could send us the genome sequence by email. Then we will do the analysis work for you.

https://academic.oup.com/database/article/doi/10.1093/database/baw084/2630454

Address of the bookmark: http://ani.mypathogen.cn/

Dot, an interactive viewer for genome-genome comparison

Jit — Sun, 14 Jan 2018 11:57:34 -0600

Dot, an interactive dot plot viewer that allows genome scientists to visualize genome-genome alignments in order to evaluate new assemblies and perform exploratory comparative genomics.

Dot supports the output of MUMmer’s nucmer aligner the most commonly used software method for aligning genome assemblies. A quick script called DotPrep.py converts the delta file to a more streamlined coordinates file with an index that enables Dot to read in more alignments in certain regions on demand.

Dot, an interactive viewer for genome-genome comparison

https://dnanexus.github.io/dot/

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

GfaViz: flexible and interactive visualization of GFA sequence graphs

Jit — Thu, 23 Jan 2020 07:33:46 -0600

GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence the name), and this remains its core application, it is more general, and able to represent many different types of sequence graphs, including scaffolding graphs, alignment graphs, variant graphs and splicing graphs.

Address of the bookmark: https://github.com/ggonnella/gfaviz

MSAProbs - Parallel and accurate multiple sequence alignment

Neel — Tue, 09 Jul 2019 23:58:44 -0500

MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. In addition, MSAProbs is optimized for shared-memory CPUs by employing a multi-threaded design, and further parallelized for distributed-memory systems using MPI to overcome high memory overhead barrier and achieve good parallel and data-size scalability.

Address of the bookmark: http://msaprobs.sourceforge.net/homepage.htm#latest

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