BOL: Related items

PEAR

Jit — Mon, 19 Dec 2016 09:28:30 -0600

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.

Address of the bookmark: http://sco.h-its.org/exelixis/web/software/pear/doc.html

PBSuite: Software for Long-Read Sequencing Data from PacBio

Jit — Mon, 27 Feb 2017 09:54:47 -0600

PBJelly - the genome upgrading tool.
PBHoney - the structural variation discovery tool

Both are contained within the PBSuite code found in downloads.

----- PBJelly -----
Read The Paper
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768

PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes.

----- PBHoney -----
Read The Paper
http://www.biomedcentral.com/1471-2105/15/180/abstract

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

Address of the bookmark: https://sourceforge.net/projects/pb-jelly/

Multi-metagenome assembly

Radha Agarkar — Fri, 03 Mar 2017 10:14:18 -0600

This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in:

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gene W. Tyson, Kåre L. Nielsen and Per .H. Nielsen

Nature Biotechnology 2013, doi: 10.1038/nbt.2579

Address of the bookmark: https://github.com/MadsAlbertsen/multi-metagenome

DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

Jit — Wed, 19 Apr 2017 10:09:51 -0500

DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

Our work is published in Scientific Reports:

Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. Sci. Rep. 6, 31900; doi: 10.1038/srep31900 (2016).

http://www.nature.com/articles/srep31900

The manual can be downloaded from:

https://github.com/yechengxi/DBG2OLC/raw/master/Manual.docx

To use precompiled versions,please go to:

https://github.com/yechengxi/DBG2OLC/tree/master/compiled

Address of the bookmark: https://github.com/yechengxi/DBG2OLC

Bacterial genome assembly !!

Jit — Fri, 05 May 2017 06:11:22 -0500

This tutorial will serve as an example of how to use free and open-source genome assembly and secondary scaffolding tools to generate high quality assemblies of bacterial sequence data. The bacterial sample used in this tutorial will be referred to simply as “Species” since it is live data. This data is paired-end data, meaning that there are forward and reverse reads, which we will designate as Sample_R1.fastq and Sample_R2.fastq, respectively.

https://github.com/jennomics/WorkflowPaper/blob/master/Genome%20Assembly%20and%20Annotation.md

Address of the bookmark: http://bioinformatics.uconn.edu/bacterial-genome-assembly-tutorial/

fragScaff: Genome Assembly with Contiguity Preserving Transposition

Jit — Mon, 14 May 2018 04:28:14 -0500

Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to >1 megabase. This software, fragScaff, leverages coincidences between the content of different pools as a source of contiguity information for scaffolding de novo genome assemblies. FragScaff is complementary to Lachesis, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps.

Further information about fragScaff, including source code, is available at:https://sourceforge.net/projects/fragscaff/files.

Manuscript describing fragScaff was published as: Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, L Gunderson K, Steemers FJ, Shendure J#. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Research 2014 Dec;24(12):2041-9. doi: 10.1101/gr.178319.114. PubMed PMID: 25327137.

Address of the bookmark: https://sourceforge.net/projects/fragscaff/files/

Sushi: An R/Bioconductor package for visualizing genomic data

Jit — Wed, 31 Aug 2016 08:29:12 -0500

Sushi: An R/Bioconductor package for visualizing genomic data

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/Sushi/inst/doc/Sushi.pdf

R-chie

Jit — Thu, 01 Sep 2016 11:47:24 -0500

R-chie allows you to make arc diagrams of RNA secondary structures, allowing for easy comparison and overlap of two structures, rank and display basepairs in colour and to also visualize corresponding multiple sequence alignments and co-variation information.
R4RNA is the R package powering R-chie, available for download and local use for more customized figures and scripting.

http://www.e-rna.org/r-chie/plot.cgi?eg=single

Address of the bookmark: http://www.e-rna.org/r-chie/plot.cgi?eg=single

SGA: String Graph Assembler

Jit — Thu, 08 Dec 2016 05:08:59 -0600

SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.

More at

https://github.com/jts/sga

SGA dependencies:
-google sparse hash library (http://code.google.com/p/google-sparsehash/)
-the bamtools library (https://github.com/pezmaster31/bamtools)
-zlib (http://www.zlib.net/)
-(optional but suggested) the jemalloc memory allocator (http://www.canonware.com/jemalloc/download.html)

Address of the bookmark: https://github.com/jts/sga

MeGAMerge: A tool to merge assembled contigs, long reads from metagenomic sequencing runs

Jit — Mon, 19 Dec 2016 09:42:15 -0600

MeGAMerge

MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)

Description

MeGAMerge is a perl based wrapper/tool that can accept any number of sequence (FASTA) files containing assembled contigs of any length in Multi-FASTA format to produce an improved contig set based on OLC based assembly. All overlap parameters (Minimum Overlap Length, Identity, etc) are user-declarable at runtime. It is written to run on Linux.

Requirements:

You will need to have the following tools installed and in $PATH, or added to $binpath in the tool:

Newbler (specifically runAssembly)
Minimus2 (part of AMOS, also requires MUMmer)

Address of the bookmark: https://github.com/LANL-Bioinformatics/MeGAMerge