BOL: Related items

GenomeRing: alignment visualization based on SuperGenome coordinates

Neel — Wed, 18 Jan 2017 10:24:10 -0600

The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. Computational tools that can visualize genome alignments in a meaningful manner are needed to help researchers gain new insights into the underlying data. Such visualizations typically are either realized in a linear fashion as in genome browsers or by using a circular approach, where relationships between genomic regions are indicated by arcs. Both methods allow for the integration of additional information such as experimental data or annotations. However, providing a visualization that still allows for a quick and comprehensive interpretation of all important genomic variations together with various supplemental data, which may be highly heterogeneous, remains a challenge.

More at https://academic.oup.com/bioinformatics/article/28/12/i7/268598/GenomeRing-alignment-visualization-based-on

Address of the bookmark: http://it.informatik.uni-tuebingen.de/?page_id=185

sockeye

Jit — Fri, 17 Feb 2017 08:51:16 -0600

This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization.

Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/sockeye/releases/1.3

ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data

Jit — Fri, 24 Feb 2017 04:55:41 -0600

ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, they report findings regarding errors in sequencing. The method can be used for whole genome shotgun (WGS) sequencing data. They also show applicability of the method for variant calling and allele dosage estimation. Results for simulated and real datasets are discussed and provide evidence that ConPADE performs well as long as enough sequencing coverage is available, or the true contig ploidy is low.

https://github.com/microsoftgenomics

Address of the bookmark: https://github.com/microsoftgenomics

splitbam: splits a BAM by chromosomes

Jit — Tue, 28 Feb 2017 09:01:28 -0600

splitbam splits a BAM by chromosomes.

Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to avoid some tools (like samtools) to crash.

Usage

java -jar splitbam.jar -p OUT/__CHROM__/__CHROM__.bam -R ref.fasta (bam|sam|stdin)

Options

-h help; This screen.
-R (indexed reference file) REQUIRED.
-u (unmapped chromosome name): default:Unmapped
-e | --empty : generate EMPTY bams for chromosome having no read mapped
-m | --mock : if option '-e', add a mock pair of sam records to the empty bam
-p (output file/bam pattern) REQUIRED. MUST contain __CHROM__ and end with .bam
-s assume input is sorted.
-x | --index create index.
-t | --tmp (dir) tmp file directory
-G (file) chrom-group file (see below)

Address of the bookmark: https://code.google.com/archive/p/jvarkit/wikis/SplitBam.wiki

Prokka: tool for the rapid annotation of prokaryotic genomes

Jit — Mon, 06 Mar 2017 03:49:57 -0600

Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.

Address of the bookmark: http://www.vicbioinformatics.com/software.prokka.shtml

COCACOLA (binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge)

Jit — Tue, 07 Mar 2017 08:50:57 -0600

COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs. Furthermore, COCACOLA seamlessly embraces customized prior knowledge to facilitate binning accuracy.

News: Python version of COCACOLA is available now!

Address of the bookmark: https://github.com/younglululu/COCACOLA

Pacbio Long Reads Compatible Software and Tools

Archana Malhotra — Wed, 15 Mar 2017 14:19:01 -0500

The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual project sites for up-to-date license information. A separate page lists commercial software.

Know of any other open source software for PacBio data? Email us.

Software categories:

Address of the bookmark: https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software

SSPACE

Jit — Fri, 05 May 2017 05:42:15 -0500

SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. Currently we offer this as a command-line tool in Perl. The input data is given by pre-assembled contig sequences (FASTA) and NGS paired-read data (Illumina/454/Solid FASTA or FASTQ). The final scaffolds are provided in FASTA format.

Address of the bookmark: https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE

Download assemblies from NCBI

Bulbul — Mon, 15 May 2017 06:02:32 -0500

A new “Download assemblies” button is now available in the Assembly database. This makes it easy to download data for multiple genomes without having to write scripts.

For example, you can run a search in Assembly and use check boxes (see left side of screenshot below) to refine the set of genome assemblies of interest. Then, just open the “Download assemblies” menu, choose the source database (GenBank or RefSeq), choose the file type, and start the download. An archive file will be saved to your computer that can be expanded into a folder containing your selected genome data files.

More at https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/08/genome-data-download-made-easy/

Genome Annotation Transfer Utility (GATU)

Jit — Mon, 29 May 2017 05:54:53 -0500

Genome Annotation Transfer Utility (GATU) was designed to facilitate quick, efficient annotation of similar genomes using genomes that have already been annotated. For example, whenever a new strain of SARS coronavirus is sequenced, it is possible, using GATU, to automatically annotate the new strain using a previously-annotated strain of SARS CoV. This saves researchers from tedious manual annotation of these sequences.

The program utilizes tBLASTn and BLASTn algorithms to map genes from the reference genome (the annotated strain) to the new sequence (the unannotated strain). The goal is to annotate the majority of the new genome’s genes in a single step. ORFs present in the target genome and absent from the reference genome are also identified; these ORFs can be further analyzed using BLAST, VGO and BBB. Afterwards, they can either be accepted for/rejected from annotation. GATU can handle multiple-exon genes as well as mature peptides. Although it was designed for use with viral genomes, GATU can also be used to help annotate larger genomes (ie. bacterial genomes).

The output is saved in GenBank, XML, or EMBL file format.

Address of the bookmark: https://virology.uvic.ca/help/tool-help/help-books/genome-annotation-transfer-utility-gatu-documentation/