BOL: Related items

Applying MinHash to cluster RNAseq samples

Neel — Thu, 26 Aug 2021 10:37:19 -0500

A kmer blog worth spending time on

Address of the bookmark: http://ivory.idyll.org/blog/2016-sourmash.html

TGNet

Shruti Paniwala — Wed, 24 Aug 2016 05:36:36 -0500

Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis.

Visualization and quality assessment of de novo genome assemblies

Citation

This software is fully described in the paper:
Riba-Grognuz, Keller, Falquet, Xenarios & Wurm (2011) Visualization and quality assessment of de novo genome assemblies.

In brief, our scripts create Cytoscape files to visualize transcript evidence that suggests adjacency between scaffolds and contigs.

Software requirements

BLAT (tested with Standalone BLAT v. 32×1). Source Binaries .
Cytoscape (tested with versions 2.7.0, 2.8.2)
a UNIX machine (tested on Mac OS X 10.6 and CentOS 4.6)

Address of the bookmark: https://github.com/ksanao/TGNet

sockeye

Jit — Fri, 17 Feb 2017 08:51:16 -0600

This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization.

Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/sockeye/releases/1.3

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/

IRscope: an online program to visualize the junction sites of chloroplast genomes

Neel — Wed, 25 Nov 2020 19:44:46 -0600

eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences.

Address of the bookmark: https://sites.google.com/g.hmc.edu/empress/home

Ribbon: Visualizing complex genome alignments and structural variation:

Jit — Wed, 29 Nov 2017 07:40:22 -0600

Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right.

Local installation:

You can install Ribbon locally from Github by following the instructions here: https://github.com/MariaNattestad/Ribbon

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

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

dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements

Rahul Nayak — Sat, 02 Dec 2017 18:25:44 -0600

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

dnaPipeTE is developped by Clément Goubert, Laurent Modolo and the TREEP team of the LBBE: http://lbbe.univ-lyon1.fr/-Equipe-Elements-transposables-.html?lang=en
You can find the original publication in GBE here: https://academic.oup.com/gbe/article/7/4/1192/533768

output examples of quantification and TE landscape (relative age) produced by dnaPipeTE

Address of the bookmark: https://github.com/clemgoub/dnaPipeTE

CroCo: A program to detect potential cross contaminations in HTS assembled transcriptomes using expression level quantification

Jit — Mon, 07 Jan 2019 18:17:44 -0600

CroCo is a program to detect cross contamination events in assembled transcriptomes using sequencing reads to determine the true origin of every transcripts.
Such cross contaminations can be expected if several RNA-Seq experiments were prepared during the same period at the same lab, or by the same people, or if they were processed or sequenced by the same sequencing service facility.
Our approach first determines a subset of transcripts that are suspiciously similar across samples using a pairwise BLAST procedure. CroCo then combine all transcriptomes into a metatranscriptome and quantifies the "expression level" of all transcripts successively using every sample read data (e.g. several species sequenced by the same lab for a particular study) while allowing read multi-mappings.
Several mapping tools implemented in CroCo can be used to estimate expression level (default is RapMap).
This information is then used to categorize each transcript in the following 5 categories :

clean: the transcript origin is from the focal sample.

cross contamination: the transcript origin is from an alien sample of the same experiment.

dubious: expression levels are too close between focal and alien samples to determine the true origin of the transcript.

low coverage: expression levels are too low in all samples, thus hampering our procedure (which relies on differential expression) to confidently assign it to any category.

over expressed: expression levels are very high in at least 3 samples and CroCo will not try to categorize it. Indeed, such a pattern does not correspond to expectations for cross contaminations, but often reflect highly conserved genes such as ribosomal gene, or external contamination shared by several samples (e.g. Escherichia coli contaminations).

Address of the bookmark: https://gitlab.mbb.univ-montp2.fr/mbb/CroCo

MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (v4) to detect variants.

Rahul Nayak — Wed, 27 Apr 2022 04:34:12 -0500

MUM&Co is able to detect:
Deletions, insertions, tandem duplications and tandem contractions (>=50bp & <=150kb)
Inversions (>=1kb) and translocations (>=10kb)

Address of the bookmark: https://github.com/SAMtoBAM/MUMandCo