BOL: Related items

Mapping NGS

Abhimanyu Singh — Tue, 02 May 2017 07:58:07 -0500

NGS data are just a bunch of sequences, you have no idea which region in the genome each sequences comes from, which gene it represents...
To know that you have to align the sequences to the reference sequence. The reference sequence is in most cases the full genome sequence but sometimes, a library of EST sequences is used.
In either way, aligning your sequence reads to the reference sequence is called mapping.

The most used mappers of DNA-seq data are BWA and Bowtie for DNA-Seq data and Tophat, STAR or HISAT for RNA-Seq data. Mappers differ in which options they can take in, how fast and how accurate they are. Bowtie is faster than BWA, but looses some sensitivity (does not map an equal amount of reads to the correct position in the genome).

Address of the bookmark: http://wiki.bits.vib.be/index.php/Mapping_of_NGS_data

Salzberg lab

Mon, 15 May 2017 05:14:01 -0500

We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with biomedical scientists to apply these methods to current problems arising in a broad spectrum of biological and medical research areas. We’re also part of the Center for Computational Biology, a group of 20+ faculty members and their labs at Johns Hopkins working on computational, statistical, and mathematical methods that can turn massive genomic data sets into biologically and clinically useful information.

https://salzberg-lab.org/

MAKER

Jitendra Narayan — Sun, 07 Feb 2016 15:59:24 -0600

MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.

More at http://www.yandell-lab.org/software/maker.html

Address of the bookmark: http://www.yandell-lab.org/software/maker.html

Stacks

Jitendra Narayan — Wed, 24 Feb 2016 15:52:30 -0600

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

More at http://catchenlab.life.illinois.edu/stacks/

Address of the bookmark: http://catchenlab.life.illinois.edu/stacks/

Linux command line exercises for NGS data processing

Jit — Wed, 22 Jun 2016 07:59:39 -0500

The purpose of this tutorial is to introduce students to the frequently used tools for NGS analysis as well as giving experience in writing one-liners. Copy the required files to your current directory, change directory (cd) to the linuxTutorial folder, and do all the processing inside:

[uzi@quince-srv2 ~/]$ cp -r /home/opt/MScBioinformatics/linuxTutorial .
[uzi@quince-srv2 ~/]$ cd linuxTutorial
[uzi@quince-srv2 ~/linuxTutorial]$

I have deliberately chosen Awk in the exercises as it is a language in itself and is used more often to manipulate NGS data as compared to the other command line tools such as grep, sed, perl etc. Furthermore, having a command on awk will make it easier to understand advanced tutorials such as Illumina Amplicons Processing Workflow.

In Linux, we use a shell that is a program that takes your commands from the keyboard and gives them to the operating system. Most Linux systems utilize Bourne Again SHell (bash), but there are several additional shell programs on a typical Linux system such as ksh, tcsh, and zsh. To see which shell you are using, type

[uzi@quince-srv2 ~/linuxTutorial]$ echo $SHELL

/bin/bash

Address of the bookmark: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/linux.html

CrossMap

Abhimanyu Singh — Mon, 05 Sep 2016 04:07:38 -0500

CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)).
It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.
CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome.
We do not recommend using CrossMap to convert genome coordinates between species.

Address of the bookmark: http://crossmap.sourceforge.net/

OrganellarGenomeDRAW

Jit — Tue, 16 Aug 2016 08:13:13 -0500

OrganellarGenomeDRAW is dedicated to convert genetic information stored in GenBank entries to graphical maps. The input text file has to be in GenBank flat file format, whereas the output format can be chosen among several formats. The application is especially optimized and adapted for the creation of high-quality, detailed circular maps of organellar genomes like the plastid genome (plastome) or the mitochondrial genome (chondriome). Nevertheless, you can upload any GenBank entry. The workflow is devided into three steps.

More at http://ogdraw.mpimp-golm.mpg.de/cgi-bin/ogdraw.pl

Address of the bookmark: http://ogdraw.mpimp-golm.mpg.de/index.shtml

TEannot

Jit — Thu, 18 Aug 2016 10:02:03 -0500

We advise to run first the TEdenovo pipeline but it is not compulsory. We suppose you begin by running the TEannot pipeline on the example provided in the directory "db/" rather than directly on your own genomic sequences. Thus, from now on, the project name is "DmelChr4".

Address of the bookmark: https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto

GeneMANIA

Jit — Mon, 22 Aug 2016 09:55:16 -0500

Faster, more accurate algorithms function prediction "GeneMANIA (Multiple Association Network Integration Algorithm)" have however been developed in recent years and are publicly available on the web, indicating the future direction of function prediction.

Address of the bookmark: http://genemania.org/

GeneValidator - Identify problems with predicted genes

Poonam Mahapatra — Fri, 26 Aug 2016 06:00:03 -0500

GeneValidator helps in identifing problems with gene predictions and provide useful information extracted from analysing orthologs in BLAST databases. The results produced can be used by biocurators and researchers who need accurate gene predictions.

If you would like to use GeneValidator on a few sequences, see our online GeneValidator Web App -http://genevalidator.sbcs.qmul.ac.uk.

If you use GeneValidator in your work, please cite us as follows:

Dragan M‡, Moghul MI‡, Priyam A, Bustos C & Wurm Y. 2016. GeneValidator: identify problems with protein-coding gene predictions. Bioinformatics, doi: 10.1093/bioinformatics/btw015.

Address of the bookmark: https://github.com/wurmlab/genevalidator