BOL: Related items

YASRA: Reference based assembler

Abhimanyu Singh — Wed, 01 Mar 2017 08:32:45 -0600

YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced. Mapping reads to reference genomes makes use of LASTZ (Harris et al), a pairwise sequence aligner compatible with BLASTZ. Special scoring sets were derived to improve the performance, both in runtime and quality for 454 and Illumina sequence reads.

YASRA uses LASTZ (http://bx.psu.edu/miller_lab for released version and http://www.bx.psu.edu/~rsharris/lastz/newer for newer version) for aligning the sequences to the reference genome. Please install LASTZ (the newest version on http://www.bx.psu.edu/~rsharris/lastz/newer) and add the LASTZ binary in your executable/binary search path before installing YASRA.

Address of the bookmark: https://github.com/aakrosh/YASRA

Carefully opt for human reference genome

biogeek — Tue, 18 Feb 2020 07:43:32 -0600

Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome.

if you map reads to GRCh38 or hg38, use the following:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

There are several other versions of GRCh37/GRCh38. What’s wrong with them? Here are a collection of potential issues:

More at http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Address of the bookmark: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

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/

Kraken: ultrafast metagenomic sequence classification using exact alignments

Jit — Mon, 27 Jun 2016 11:01:44 -0500

Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.

Krona

https://sourceforge.net/p/krona/home/krona/

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053813/

NovelSeq: Novel Sequence Insertion Detection

Neel — Fri, 09 Jun 2017 04:31:30 -0500

The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.

http://novelseq.sourceforge.net/Home

Paper at https://www.ncbi.nlm.nih.gov/pubmed/20385726

Address of the bookmark: http://novelseq.sourceforge.net/Home

ASAR: Advanced metagenomic Sequence Analysis in R

Jit — Mon, 09 Jul 2018 05:20:50 -0500

An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

Address of the bookmark: https://github.com/Askarbek-orakov/ASAR

Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome

BioStar — Wed, 22 Jul 2020 10:11:13 -0500

We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi.

More at https://pubmed.ncbi.nlm.nih.gov/20494974/

Address of the bookmark: http://www.sequenceontology.org/cgi-bin/soba.cgi

ULTRA (ULTRA Locates Tandemly Repetitive Areas) : Effective Labeling of Repetitive Genomic Sequence

Abhi — Sat, 08 Jun 2024 16:03:39 -0500

ULTRA is a tool to find and annotate tandem repeats inside genomic sequence. It is able to find repeats of any length and of any period (up to a maximum period of 4000). It can find highly decayed repeats missed by other software, and it will also be able to find very large repeats in highly repetitive sequence, regardless of the size of sequence or length of repeats. ULTRA offers meaningful annotation scores and can produce annotation P-values at user request.

More at https://www.biorxiv.org/content/10.1101/2024.06.03.597269v1

Address of the bookmark: https://github.com/TravisWheelerLab/ULTRA

Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence

Jit — Thu, 23 Nov 2017 08:37:15 -0600

Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast).

Address of the bookmark: https://sourceforge.net/projects/taxoblast/files/

Circoletto: visualizing sequence similarity with Circos

Jit — Fri, 09 Feb 2018 10:23:40 -0600

Circoletto, an online visualization tool based on Circos, which provides a fast, aesthetically pleasing and informative overview of sequence similarity search results.

Online version and downloadable software package for offline use (source code in PERL) freely available at http://bat.ina.certh.gr/tools/circoletto/

Contact:ndarz@certh.gr

Address of the bookmark: http://tools.bat.infspire.org/circoletto/