BOL: Related items

GFinisher: a new strategy to refine and finish bacterial genome assemblies

Jit — Thu, 26 Jul 2018 09:31:55 -0500

GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references.

java -Xms2G -Xmx4G -jar GenomeFinisher.jar  \
    -i target_contigs.fasta  \
    -ds alternative_assemblies.fasta -ref reference.fasta  \
    -o outputDirectory

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

Synima: a Synteny imaging tool for annotated genome assemblies

Abhimanyu Singh — Tue, 30 Oct 2018 10:49:13 -0500

Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Address of the bookmark: https://github.com/rhysf/Synima

ANItools web: a web tool for fast genome comparison within multiple bacterial strains

Jit — Wed, 14 Nov 2018 04:34:23 -0600

ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you could send us the genome sequence by email. Then we will do the analysis work for you.

https://academic.oup.com/database/article/doi/10.1093/database/baw084/2630454

Address of the bookmark: http://ani.mypathogen.cn/

ARCS: scaffolding genome drafts with linked reads

Jit — Mon, 17 Dec 2018 17:40:28 -0600

ARCS requires two input files:

Draft assembly fasta file
Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to produce this interleaved file)

Address of the bookmark: https://github.com/bcgsc/ARCS/

LTR_retriever: accurately identifies and annotates LTR retrotransposons and use LAI to evaluates the continuity of genome assemblies.

Neel — Sun, 13 Jan 2019 07:14:31 -0600

LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, and/or MGEScan-LTR and generating non-redundant LTR-RT library for genome annotations.

By default, the program will generate whole-genome LTR-RT annotation and the LTR Assembly Index (LAI) for evaluations of the assembly continuity of the input genome. Users can also run LAI separately (see Usage).

Address of the bookmark: https://github.com/oushujun/LTR_retriever

Liu Lab

Tue, 04 Feb 2020 06:27:02 -0600

Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance.

https://liulab-dfci.github.io/software/

Svardal lab

Sat, 20 Feb 2021 10:01:19 -0600

In the Svardal lab they are interested how the astonishing natural diversity we see on earth came into being, by which forces it formed and how it is changing today. Hence, they are trying to understand the process of evolution, with mathematical models and through the analysis of genome sequencing data.

Genomes, and in particular differences between them, are a crucial source of information to understand evolution and biology in general. They provide a record of the evolutionary past of populations, their relatedness patterns, their demography, and their adaptations.

More at https://www.uantwerpen.be/en/staff/hannes-svardal/svardal-lab/

Calling variants in non-diploid systems

Neel — Sat, 26 Jun 2021 15:37:49 -0500

The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA although the same approaches will work equally good on viral and bacterial genomes (Rebolledo-Jaramillo et al. 2014, Li et al. 2015).

Address of the bookmark: https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html

GenomeTools: The versatile open source genome analysis software

Neel — Wed, 02 Feb 2022 04:00:21 -0600

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.

If you are interested in gene prediction, have a look at GenomeThreader.

http://genometools.org/pub/

Address of the bookmark: http://genometools.org/

CrossMap: program for genome coordinates conversion between different assemblies

Rahul Nayak — Tue, 25 Jan 2022 17:59:32 -0600

CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF.

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