BOL: Related items

cutadapt

Radha Agarkar — Fri, 13 May 2016 04:54:50 -0500

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but often you don’t want them to be in your reads.

Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Also, paired-end reads and even colorspace data is supported. If you want, you can also just demultiplex your input data, without removing adapter sequences at all.

Cutadapt comes with an extensive suite of automated tests and is available under the terms of the MIT license.

If you use cutadapt, please cite DOI:10.14806/ej.17.1.200 .

Address of the bookmark: https://cutadapt.readthedocs.io/en/stable/installation.html#quickstart

GAM-NGS: genomic assemblies merger for next generation sequencing

Jit — Fri, 19 May 2017 07:44:14 -0500

GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based projects. With more than 20 available assemblers it is hard to select the best tool. In this context we propose a tool that improves assemblies (and, as a by-product, perhaps even assemblers) by merging them and selecting the generating that is most likely to be correct.

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

simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data

Jit — Tue, 28 Nov 2017 06:49:11 -0600

simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from more esoteric sources of noise that may be present in real data ("dust", bubbles, merged clusters, sequence-heterogeneous clusters, etc). Many of these additional sources may optionally applied.

simNGS takes fasta format sequences and a file describing the covariance of noise between bases and cycles observed in an actual run of the machine, randomly generates noisy intensities representing the signals for the sequence at each cycle and calculates likelihoods for all possible base calls.

Address of the bookmark: https://www.ebi.ac.uk/goldman-srv/simNGS/

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Poonam Mahapatra — Mon, 26 Aug 2019 18:07:33 -0500

Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast, Saccharomyces cerevisiae, has many isolates currently being sequenced with long reads.

Address of the bookmark: https://github.com/yjx1217/LRSDAY

Genobuntu: Package for Next Generation Sequencing and Genome Assembly

BioStar — Mon, 18 May 2020 16:47:56 -0500

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Features

Velvet
MiB
SSAKE
EULER
VCAKE
ABySS
ALLPATHS
Celera
SHARCGS
Allpaths
IDBA
TAIPAN
Edena
SOAPdenovo
Maq
IDBA-UD
No. of Reads present in the Ref. Seq.
ART NGS Reads Simulator
HiTEC, FASTQC
Minimum Description Length
SOAPaligner
Sequencing Read Archive Toolkit

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

Structure of Binary files used for storing sequencing data-bam and sff

Rahul Agarwal — Sun, 11 Aug 2013 14:29:49 -0500

Many times bioinformatician needs to parse binary files like bam and sff. Advantage of binary files is that they occupy less space in memory with maximum information content.

Link for those who looking for structure of Bam and sff file:

Bam:

http://samtools.sourceforge.net/SAMv1.pdf (from page 12)

sff file (for Ion torrent and 454 files):

http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff

Binary file Editor and Viewer:

http://mh-nexus.de/en/hxd/

Illumina reveals first dataset of long reads

Rahul Agarwal — Fri, 23 Aug 2013 06:29:14 -0500

With the help of Moleculo technology , acquired by Illumina releases new service for long reads sequencing i.e., FastTrack Long Reads.

Average read length is around 8,500 base pairs in release dataset. Best thing about this, there is not much effect on cost and quality of data.

You can also check following pages for publications on long reads and more:

http://www.illumina.com/services/long-read-sequencing-service.ilmn

http://blog.basespace.illumina.com/2013/07/22/first-data-set-from-fasttrack-long-reads-early-access-service/

New born babies get ready to know their whole genome soon!!!

Rahul Agarwal — Thu, 05 Sep 2013 07:24:02 -0500

USA launch a pilot projects to examine medical information of newborn baby, which are being funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) and the National Human Genome Research Institute (NHGRI), both parts of the National Institutes of Health.

Awards of $5 million to four grantees have been made in fiscal year 2013 under the Genomic Sequencing and Newborn Screening Disorders research program. The program will be funded at $25 million over five years, as funds are made available.

"Hundreds of US babies will be pioneers in genomic medicine through a US$25-million programme to sequence their genomes soon after they are born."

Source:

http://blogs.nature.com/news/2013/09/scientists-to-sequence-hundreds-of-newborns-genomes.html

http://www.genome.gov/27554919

Role of microbes in forensic science

Rahul Agarwal — Sun, 29 Sep 2013 10:07:20 -0500

"Studies on decomposing mice suggest that the microbial content of a corpse can offer clues as to how old a body is and the approximate time that death occurred."

Read more: http://www.digitaljournal.com/article/359185#ixzz2gIJFVHRo

http://www.colorado.edu/news/releases/2013/09/24/new-cu-boulder-led-study-finds-%E2%80%98microbial-clock%E2%80%99-may-help-determine-time

Paper:

http://www.elifesciences.org/wp-content/uploads/2013/09/eLife.01104_INPRESS.pdf

The First 50 Plant Genomes

Rahul Agarwal — Mon, 21 Oct 2013 11:19:35 -0500

Plant scientists can exploit available 50 plant complete genomic data for their resequencing or other related projects for understanding the genetic mechanism behind their different traits and molecular evolution. Complete information about these plant genomes given in paper link.

https://www.crops.org/publications/tpg/articles/6/2/plantgenome2013.03.0001in

Address of the bookmark: https://www.crops.org/publications/tpg/pdfs/6/2/plantgenome2013.03.0001in