BOL: Related items

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

Redundans

Jit — Thu, 01 Sep 2016 08:28:11 -0500

Redundans pipeline assists an assembly of heterozygous genomes.
Program takes as input assembled contigs, paired-end and/or mate pairs sequencing libraries and returns scaffolded homozygous genome assembly, that should be less fragmented and with total size smaller than the input contigs. In addition, Redundans will automatically close the gaps resulting from genome assembly or scaffolding more details.

The pipeline consists of three steps/modules:

redundancy reduction: detection and selectively removal of redundant contigs from an initial de novo assembly
scaffolding: joining of genome fragments using paired-end and/or mate-pairs reads
gap closing

Redundans is:

fast & lightweight, multi-core support and memory-optimised, so it can be run even on the laptop for small-to-medium size genomes
flexible toward many sequencing technologies (Illumina, 454 or Sanger) and library types (paired-end, mate pairs, fosmids)
modular: every step can be ommited or replaced by another tools

Address of the bookmark: https://github.com/Gabaldonlab/redundans

SWALO

Jit — Wed, 30 Nov 2016 05:06:05 -0600

SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing.

Download

Git repository of SWALO is at https://github.com/atifrahman/SWALO.

Address of the bookmark: https://atifrahman.github.io/SWALO/

Cutadapt

Bulbul — Wed, 14 Dec 2016 09:59:52 -0600

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

More at https://github.com/marcelm/cutadapt

Address of the bookmark: http://cutadapt.readthedocs.io/en/stable/guide.html

GARM:Genome Assembly, Reconciliation and Merging

Jit — Mon, 19 Dec 2016 06:03:02 -0600

The pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on Debian, Ubuntu, Fedora and BioLinux distributions. The method merges contigs or scaffolds from different assemblers using the same or different sequencing technologies. When scaffolds are provided, a process of finding probable compressions or extensions (CE) problems in the assemblies can be per-formed; contigs are joined back into scaffolds after gap recalculation

Address of the bookmark: http://garm-meta-assem.sourceforge.net/

quickmerge: A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

Jit — Mon, 19 Dec 2016 10:23:36 -0600

quickmerge uses a simple concept to improve contiguity of genome assemblies based on long molecule sequences, often with dramatic outcomes. The program uses information from assemblies made with illumina short reads and PacBio long reads to improve contiguities of an assembly generated with PacBio long reads alone. This is counterintuitive because illumina short reads are not typically considered to cover genomic regions which PacBio long reads cannot. Although we have not evaluated this program for assemblies generated with Oxford nanopore sequences, the program should work with ONP-assemblies too.

Address of the bookmark: https://github.com/mahulchak/quickmerge

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

CrossMap

Jitendra Narayan — Mon, 08 Feb 2016 15:47:00 -0600

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.

More at http://crossmap.sourceforge.net/

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

Easyfig

Poonam Mahapatra — Fri, 29 Apr 2016 05:49:39 -0500

Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig. Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

More at http://easyfig.sourceforge.net/

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

SPAdes

Abhimanyu Singh — Tue, 19 Apr 2016 08:37:08 -0500

SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8, 2016 and can be downloaded from http://bioinf.spbau.ru/en/spades.

Manual at http://spades.bioinf.spbau.ru/release3.7.1/manual.html

Address of the bookmark: http://bioinf.spbau.ru/spades