BOL: Related items

Filtlong: quality filtering tool for long reads

Radha Agarkar — Wed, 13 May 2020 10:23:55 -0500

Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.

Filtlong builds into a stand-alone executable:

git clone https://github.com/rrwick/Filtlong.git
cd Filtlong
make -j
bin/filtlong -h

Address of the bookmark: https://github.com/rrwick/Filtlong

AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads

Rahul Nayak — Sun, 14 Mar 2021 09:42:47 -0500

AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome.

More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/6146772

Address of the bookmark: https://github.com/huangs001/AlignGraph2

Steps to find palindrome in genomes !

BioStar — Thu, 09 Mar 2023 02:56:54 -0600

Palindromes are sequences of nucleotides that read the same backward as forward. They can be present in genomes and have various biological functions. Here are some methods for discovering palindromes in genomes:

Direct sequence search: One of the simplest ways to discover palindromes is to search the genome sequence directly for palindromic sequences using pattern matching tools, such as regular expressions or string algorithms. This approach can be useful for discovering simple palindromes, but may miss more complex palindromic structures.
Dot plot analysis: Dot plot analysis is a graphical method that can be used to identify palindromic regions in a genome. It involves plotting the genome sequence against itself and examining the diagonal patterns that emerge. Palindromic regions will appear as symmetrical patterns along the diagonal.
Restriction enzyme analysis: Some restriction enzymes, such as EcoRI and HindIII, recognize palindromic sequences and cleave DNA at these sites. By digesting the genome with these enzymes and examining the resulting fragments, palindromic regions can be identified.
Next-generation sequencing: High-throughput sequencing technologies, such as PacBio and Oxford Nanopore, can generate long reads that can span entire palindromic regions. By mapping these reads to the genome, palindromic regions can be identified and characterized.
Comparative genomics: Comparing the genomes of related species can also reveal palindromic regions that are conserved across evolutionarily divergent lineages. This approach can help identify functional palindromes that are under selective pressure.

Overall, the discovery of palindromic sequences in genomes can be accomplished using a variety of methods, each with their own advantages and limitations. A combination of these methods can provide a comprehensive understanding of the palindromic landscape of a genome.

Trimmomatic: A flexible read trimming tool for Illumina NGS data

Jit — Fri, 15 Apr 2016 05:58:53 -0500

Paired End:

java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

This will perform the following:

Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10)
Remove leading low quality or N bases (below quality 3) (LEADING:3)
Remove trailing low quality or N bases (below quality 3) (TRAILING:3)
Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15)
Drop reads below the 36 bases long (MINLEN:36)

More at http://www.usadellab.org/cms/?page=trimmomatic

Address of the bookmark: http://www.usadellab.org/cms/?page=trimmomatic

segemehl

Anjana — Tue, 10 May 2016 08:10:15 -0500

segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA).

More at http://www.bioinf.uni-leipzig.de/Software/segemehl/

Manual http://www.bioinf.uni-leipzig.de/Software/segemehl/segemehl_manual_0_1_7.pdf

Address of the bookmark: http://hoffmann.bioinf.uni-leipzig.de/LIFE/segemehl.html

SpeedSeq

Jit — Fri, 20 Jan 2017 06:05:43 -0600

A flexible framework for rapid genome analysis and interpretation

C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth (2015). doi:10.1038/nmeth.3505.

http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html

Address of the bookmark: https://github.com/hall-lab/speedseq

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/

BEAR: Better Emulation for Artificial Reads

BioStar — Sat, 06 Jul 2024 04:27:53 -0500

Created by Stephen Johnson, Brett Trost, Dr. Jeffrey R. Long, Dr. Anthony Kusalik University of Saskatchewan, Department of Computer Science

BEAR is intended to be an easy-to-use collection of scripts for generating simulated WGS metagenomic reads with read lengths, quality scores, error profiles, and species abundances derived from real user-supplied WGS data.

Address of the bookmark: https://github.com/sej917/BEAR

Rolf Backofen Lab

Thu, 18 Jul 2013 13:51:23 -0500

The research interest of this group include constraint programming, structure prediction in simplified protein models, investigation of protein energy landscapes, detection of RNA sequence/structure motifs, prediction and evaluation of alternative splice forms, description and detection of regulatory sequences.

Link @ http://www.bioinf.uni-freiburg.de/

RNA Sequencing Helps Identify Functional Variants from GWAS

Andaleeb — Fri, 22 Nov 2013 21:33:33 -0600

For Alzheimer’s and other complex disorders, mining the genome for disease-associated variants is no longer the obstacle. The challenge nowadays is figuring out how the identified loci relate to disease. As reported last month in Nature and its associated journals, advances in high-throughput RNA sequencing are providing new tools for understanding how disease loci influence gene expression—a starting point for understanding their connection to pathogenesis.

Address of the bookmark: http://schizophreniaforum.org/new/detail.asp?id=1953