BOL: Related items

SciLifeLab tutorial for bioinformatics analysis !

Jit — Tue, 17 Apr 2018 04:33:00 -0500

SciLifeLab is a national center for molecular biosciences with focus on health and environmental research.

Courses

Old courses (2012-2014)

LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)

Jit — Mon, 14 May 2018 04:26:30 -0500

LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly.

Further information about LACHESIS, including source code, documentation and a user's guide are available at: http://shendurelab.github.io/LACHESIS.

Manuscript describing LACHESIS was published as: Burton JN#, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J#. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nature Biotechnology 2013 Dec;31(12):1119-25. doi: 10.1038/nbt.272. PubMed PMID: 24185095.

http://shendurelab.github.io/LACHESIS/

Address of the bookmark: http://shendurelab.github.io/LACHESIS/

Levenshtein and Damerau-Levenshtein distance !

Surabhi Chaudhary — Tue, 28 Sep 2021 04:38:55 -0500

Levenshtein Distance

Also known as Edit Distance, it is the number of transformations (deletions, insertions, or substitutions) required to transform a source string into the target one. For example, if the target term is “book” and the source is “back”, you will need to change the first “o” to “a” and the second “o” to “c”, which will give us a Levenshtein Distance of 2.Edit Distance is very easy to implement, and it is a popular challenge during code interviews

Additionally, some frameworks also support the Damerau-Levenshtein distance:

Damerau-Levenshtein distance

It is an extension to Levenshtein Distance, allowing one extra operation: Transposition of two adjacent characters:

Ex: TSAR to STAR

Damerau-Levenshtein distance = 1 (Switching S and T positions cost only one operation)

Levenshtein distance = 2 (Replace S by T and T by S)

RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs

Jit — Sun, 27 Oct 2019 00:57:23 -0500

Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019.

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
Intact ordering and orienting of contigs.
Misassembly correction
GFF lift-over
Structural variant calling with and integrated version of Assemblytics
Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable Elements detection and annotation in Genome Assemblies

LEGE — Sat, 20 Sep 2025 09:34:04 -0500

HiTE is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a greater number of full-length TEs.

panHiTE

We have developed panHiTE, a comprehensive and accurate pipeline for TE detection in large-scale population genomes. It has been successfully applied to hundreds of plant population genomes, demonstrating its effectiveness and scalability.

For detailed instructions, please refer to the panHiTE tutorial.

Address of the bookmark: https://github.com/CSU-KangHu/HiTE

DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication

Jit — Tue, 14 Nov 2017 10:26:16 -0600

We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.

Availability and Implementation

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Address of the bookmark: https://dfast.nig.ac.jp/

JBrowse: Embeddable genome browser built completely with JavaScript and HTML5

Jit — Fri, 29 Jun 2018 09:19:56 -0500

JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes and deep-coverage sequencing. Quickly open and view data files on your computer without uploading them to any server. Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with either .tbi or .idx index), REST, and more. BAM, BigBed, BigWig, and VCF data are displayed directly from chunks of the compressed binary files, no conversion needed. Includes an optional “faceted” track selector (see demo) suitable for large installations with thousands of tracks. Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance. Can run as a stand-alone app on OSX and Windows using the Electron platform Highly extensible plugin architecture, with a large plugin registry of existing examples here https://gmod.github.io/jbrowse-registry https://jbrowse.org/

Address of the bookmark: https://github.com/GMOD/jbrowse

fragScaff: Genome Assembly with Contiguity Preserving Transposition

Jit — Mon, 14 May 2018 04:28:14 -0500

Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to >1 megabase. This software, fragScaff, leverages coincidences between the content of different pools as a source of contiguity information for scaffolding de novo genome assemblies. FragScaff is complementary to Lachesis, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps.

Further information about fragScaff, including source code, is available at:https://sourceforge.net/projects/fragscaff/files.

Manuscript describing fragScaff was published as: Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, L Gunderson K, Steemers FJ, Shendure J#. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Research 2014 Dec;24(12):2041-9. doi: 10.1101/gr.178319.114. PubMed PMID: 25327137.

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

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

BioStar — Fri, 07 Sep 2018 05:19:06 -0500

P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides another practical alternative to existing mate-pair_based approaches or other Protein-based approaches (for instance, PEP_scaffolder ) for scaffolding genome sequences. The most important feature of this method is to improve the completeness of gene regions and long-coding gene regions (for instance, circRNA).

Address of the bookmark: http://www.fishbrowser.org/software/P_RNA_scaffolder/#

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

BOL: Related items

SciLifeLab tutorial for bioinformatics analysis !

Courses

Metagenomics Workshop

Introduction to Bioinformatics Using NGS Data

Introduction to Genome Annotation

De Novo Genome Assembly

RNA-seq course

R Programming Foundations for Life Scientists

Single cell RNA sequencing analysis