BOL: Related items

QuorUM: An Error Corrector for Illumina Reads

BioStar — Tue, 04 Feb 2020 23:26:55 -0600

We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is efficiently implemented making use of current multi-core computing architectures and it is suitable for large data sets (1 billion bases checked and corrected per day per core)

Address of the bookmark: http://www.genome.umd.edu/

EAGLER: a scaffolding tool for long reads.

Jit — Mon, 04 Jun 2018 05:26:03 -0500

EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nanopore reads.

The tool should be compatible with most UNIX flavors and has been successfully tested on the following operating systems:

Mac OS X 10.11.1
Mac OS X 10.10.3
Ubuntu 14.04 LTS

https://bib.irb.hr/datoteka/844447.Diplomski_2015_Luka_terbi.pdf

Address of the bookmark: https://github.com/mculinovic/EAGLER

Long read assembly workshop !

Rahul Nayak — Thu, 04 Oct 2018 17:23:18 -0500

This is a tutorial for a workshop on long-read (PacBio) genome assembly.

It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and correcting the assembly with short-read Illumina data.

Please comment if you know any other long read addembly tutorial.

Address of the bookmark: http://sepsis-omics.github.io/tutorials/modules/cmdline_assembly_v2/

HASLR: a tool for rapid genome assembly of long sequencing reads

LEGE — Fri, 31 Jan 2020 05:50:15 -0600

HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample.

Address of the bookmark: https://github.com/vpc-ccg/haslr

Biological databases !

BioStar — Wed, 12 Feb 2020 01:16:29 -0600

Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

Abhi — Tue, 05 Sep 2023 07:31:35 -0500

MitoHiFi v3.2 is a python pipeline distributed under MIT License !

MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project (DToL)

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05385-y

Address of the bookmark: https://github.com/marcelauliano/MitoHiFi

Understanding PacBio

Jitendra Narayan — Fri, 24 Feb 2017 10:17:36 -0600

This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you get started with your data processing, as well as information for specialized applications.

Training Resources:

Specialized Applications:

Address of the bookmark: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki

SGA: String Graph Assembler

Jit — Thu, 08 Dec 2016 05:08:59 -0600

SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.

More at

https://github.com/jts/sga

SGA dependencies:
-google sparse hash library (http://code.google.com/p/google-sparsehash/)
-the bamtools library (https://github.com/pezmaster31/bamtools)
-zlib (http://www.zlib.net/)
-(optional but suggested) the jemalloc memory allocator (http://www.canonware.com/jemalloc/download.html)

Address of the bookmark: https://github.com/jts/sga

Understanding Greedy Algorithms

Jit — Mon, 12 Dec 2016 04:37:40 -0600

Learning greedy algo for biologist.

https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/

This webpage is also useful for the same:

http://learninglover.com/examples.php?id=59

http://www.cs.rpi.edu/~magdon/ps/conference/super_biokdd.pdf

https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf

http://schatzlab.cshl.edu/teaching/AssemblyClass/01.%20Assembly%20Intro.pdf

http://lsl.sinica.edu.tw/Services/Class/files/20150612449.pdf

http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_scs.pdf

https://www2.eecs.berkeley.edu/Pubs/TechRpts/2016/EECS-2016-43.pdf

Address of the bookmark: https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/

GAM-NGS: genomic assemblies merger for next generation sequencing

Jit — Mon, 19 Dec 2016 06:07:05 -0600

GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two assemblies representing the same genomic locus (called blocks) are identified through reads' alignments and stored in a weightedgraph. The merging phase is carried out with the help of this weighted graph that allows an optimal resolution of local problematic regions.

Address of the bookmark: https://github.com/vice87/gam-ngs