BOL: Related items

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/

NCBI Prokaryotic Genome Annotation Pipeline

Jit — Tue, 16 May 2017 08:56:03 -0500

NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume. You can find a more detailed description of the new version of the pipeline in NCBI Handbook chapter. NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

https://www.ncbi.nlm.nih.gov/genome/annotation_prok/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/

GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments

Shruti Paniwala — Mon, 11 Jun 2018 05:43:44 -0500

GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap closure. We demonstrate with sequencing data from various organisms that the gap-closing accuracy of GMcloser is 3–100-fold higher than those of other available tools, with similar efficiency. https://academic.oup.com/bioinformatics/article/31/23/3733/209212

Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/23/3733/209212

SIMBA: a Genome Assembly Project Management System

Neel — Thu, 29 Nov 2018 08:52:25 -0600

SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

Address of the bookmark: http://ufmg-simba.sourceforge.net/

Genome Assembly Workshop 2020

Jit — Wed, 25 Aug 2021 04:30:32 -0500

Our team offers custom bioinformatics services to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software. We replicate standard analysis pipelines (best practices) when appropriate, and/or develop novel applications and pipelines when needed, however we always emphasize biological interpretation of the data.

More at https://ucdavis-bioinformatics-training.github.io/

Address of the bookmark: https://ucdavis-bioinformatics-training.github.io/2020-Genome_Assembly_Workshop/snakemake/snakemake_intro

ALE: Assembly Likelihood Estimator

BioStar — Wed, 08 Mar 2023 01:39:33 -0600

Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.

Address of the bookmark: https://github.com/sc932/ALE

nQuire: a statistical framework for ploidy estimation using next generation sequencing

Jit — Thu, 04 Oct 2018 05:23:59 -0500

nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuireunder the MIT license.

Address of the bookmark: https://github.com/clwgg/nQuireunder

vt: a variant tool set that discovers short variants from Next Generation Sequencing data.

Jit — Tue, 28 Jan 2020 03:44:43 -0600

vt is a variant tool set that discovers short variants from Next Generation Sequencing data.

https://genome.sph.umich.edu/wiki/Vt

https://github.com/atks/vt

Address of the bookmark: https://genome.sph.umich.edu/wiki/Vt

DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication

Jit — Tue, 14 Nov 2017 10:26:16 -0600

We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.

Availability and Implementation

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Address of the bookmark: https://dfast.nig.ac.jp/

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

Jit — Tue, 12 Jun 2018 08:14:41 -0500

P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs.

Address of the bookmark: http://www.fishbrowser.org/software/P_RNA_scaffolder/