BOL: Related items

PAired-eND Assembler for DNA sequences

Neel — Wed, 06 Apr 2016 05:25:34 -0500

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

More at https://github.com/neufeld/pandaseq

Address of the bookmark: https://github.com/neufeld/pandaseq

SCALCE

Surabhi Chaudhary — Fri, 15 Apr 2016 05:09:51 -0500

SCALCE (/skeɪlz/, a.k.a. boosting Sequence Compression Algorithms using Locally ConsistentEncoding) is a tool for compressing FASTQ files. It is designed specifically for the Illumina-generated FASTQ files, but supports any valid FASTQ with consistent read lengths.

More at http://sfu-compbio.github.io/scalce/

Address of the bookmark: http://sfu-compbio.github.io/scalce/

CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.

Jit — Tue, 26 Apr 2016 11:38:10 -0500

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered.

Canu is a hierachical assembly pipeline which runs in four steps:

Detect overlaps in high-noise sequences using MHAP
Generate corrected sequence consensus
Trim corrected sequences
Assemble trimmed corrected sequences

Read the documentation

New release https://github.com/marbl/canu/releases

Address of the bookmark: https://github.com/marbl/canu

Platanus

Jit — Fri, 13 May 2016 05:12:40 -0500

Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of
highly heterozygous diploids from massively parallel shotgun sequencing data.

The latest version is 1.2.4.

To cite Platanus, please use the following:

Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Genome Res. 2014 Aug;24(8):1384-95. doi: 10.1101/gr.170720.113. [abstract | full text]

Address of the bookmark: http://platanus.bio.titech.ac.jp/

Blobology

Jit — Mon, 13 Jun 2016 10:18:33 -0500

Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step

Blaxter Lab, Institute of Evolutionary Biology, University of Edinburgh

Goal: To create blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step.

This repository accompanies the paper:
Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots. Sujai Kumar, Martin Jones, Georgios Koutsovoulos, Michael Clarke, Mark Blaxter
(submitted 2013-10-01 to Frontiers in Bioinformatics and Computational Biology special issue : Quality assessment and control of high-throughput sequencing data).

It contains bash/perl/R scripts for running the analysis presented in the paper to create a preliminary assembly, and to create and collate GC content, read coverage and taxon annotation for the preliminary assembly, which can be visualised, such as Figure 2a from the paper showing TAGC plots/blobplots for Caenorhabditis sp. 5:

Address of the bookmark: https://github.com/blaxterlab/blobology

KisSplice

Jit — Tue, 16 Aug 2016 08:34:19 -0500

KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads.

KisSplice is not a full-length transcriptome assembler. This means that it will output the variable regions of the transcripts, not reconstruct them entirely.

KisSplice comes as a workflow, with several possible post-treatments meant to facilitate the analysis of the results. The choice of the post-treatment depends on the availability of a reference genome/transcriptome and on the need to perform a differential analysis, as summarised in the following table.

Address of the bookmark: http://kissplice.prabi.fr/

A5-miseq

Jit — Thu, 18 Aug 2016 04:05:23 -0500

_A5-miseq_ is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running _A5-miseq_.

Point to note:

There are many situations where A5-miseq is not the right tool for the job. In order to produce accurate results, A5-miseq requires Illumina data with certain characteristics. A5-miseq will likely not work well with Illumina reads shorter than around 80nt, or reads where the base qualities are low in all or most reads before 60nt. A5-miseq assumes it is assembling homozygous haploid genomes. Use a different assembler for metagenomes and heterozygous diploid or polyploid organisms. Use a different assembler if a tool like FastQC reports your data quality is dubious. You have been warned! Datasets consisting solely of unpaired reads are not currently supported.

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

Kraken: ultrafast metagenomic sequence classification using exact alignments

Jit — Mon, 27 Jun 2016 11:01:44 -0500

Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.

Krona

https://sourceforge.net/p/krona/home/krona/

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053813/

Fancy Oneliner for Bioinformatics !!

Poonam Mahapatra — Thu, 07 Jul 2016 12:05:50 -0500

This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you follow the same naming conventions and folder structures as we have. We are sharing these codes with the intention that if they are useful and help you in your analyses, then we will be appropriately credited as considerable effort has been put into devising them.

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

MEGAN6

Neel — Mon, 25 Jul 2016 05:45:22 -0500

Microbiome analysis using a single application

MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application.

Taxonomic analysis using the NCBI taxonomy or a customized taxonomy such as SILVA
Functional analysis using InterPro2GO, SEED, eggNOG or KEGG
Bar charts, word clouds, Voronoi tree maps and many other charts
PCoA, clustering and networks
Supports metadata
MEGAN parses many different types of input

Why use MEGAN6?

The software is:

Easy to use. MEGAN6 is a single application and all features are available through menus, toolbars and graphics. No scripting skills required.
Powerful. MEGAN6 allows you to work with hundreds of samples containing hundreds of millions of sequencing reads. Blast-like analysis can be performed using DIAMOND.
Comprehensive. MEGAN6 offers a large range of analysis tools, and is under active development.

Address of the bookmark: https://ab.inf.uni-tuebingen.de/software/megan6