1. Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together.
2. Reducing/removing reference bias as compared to mapping based approaches.

The software is designed to work in situations where a whole-genome assembly is not the objective, but rather when the researcher wishes to assemble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by breaking the reads into small, manageable subsets which can then be assembled quickly and efficiently in parallel. Applications include those in which the researcher wishes to de novo assemble specific content and a set of semi-similar reference targets is available to initialize the assembly process.

https://ibest.github.io/ARC/

Address of the bookmark: https://ibest.github.io/ARC/

https://www.nature.com/articles/nm.3975

Address of the bookmark: https://www.nature.com/articles/nm.3975

Here is an illustration of this pipeline:

Address of the bookmark: https://github.com/BGI-Qingdao/SLR-superscaffolder

Address of the bookmark: https://github.com/ryanmelnyk/PyParanoid

https://github.com/ncbi/JUDI

Address of the bookmark: https://github.com/ncbi/JUDI

Bactopia was inspired by Staphopia, a workflow we (Tim Read and myself) released that is targeted towards Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start.

Bactopia uses Nextflow to manage the workflow, allowing for support of many types of environments (e.g. cluster or cloud). Bactopia allows for the usage of many public datasets as well as your own datasets to further enhance the analysis of your sequencing. Bactopia only uses software packages available from Bioconda and Conda-Forge to make installation as simple as possible for all users.

To highlight the use of Bactopia and Bactopia Tools, we performed an analysis of 1,664 public Lactobacillus genomes, focusing on Lactobacillus crispatus, a species that is a common part of the human vaginal microbiome. The results from this analysis are published in mSystems under the title: Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Address of the bookmark: https://bactopia.github.io/latest/

Address of the bookmark: https://github.com/Dfam-consortium/TETools

The GO provides core biological knowledge representation for modern biologists, whether computationally or experimentally based. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Although extensively used in data analysis workflows, and widely incorporated into numerous data analysis platforms and applications, the general user of GO resources often misses fundamental distinctions about GO structures, GO annotations, and what can and can not be extrapolated from GO resources. Here are ten quick tips for using the Gene Ontology.

Read "Ten Quick Tips for Using the Gene Ontology" at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003343

Following are the most commonly used old and new GO term enrichment determination tools. These tools are recommended to people working in a wet-lab.

CLASSIFI (Department of Pathology, UT Southwestern Medical Center)

CLASSIFI (Cluster Assignment for Biological Inference) is a data-mining tool that can be used to identify significant co-clustering of genes with similar functional properties (e.g. cellular response to DNA damage). Briefly, CLASSIFI uses the Gene OntologyTM (GO) gene annotation scheme to define the functional properties of all genes/probes in a microarray data set, and then applies a cumulative hypergeometric distribution analysis to determine if any statistically significant gene ontology co-clustering has occurred.

http://pathcuric1.swmed.edu/pathdb/classifi.html

EasyGO (China Agricultural University)

EasyGO is designed to automate enrichment job for experimental biologists to identify enriched Gene Ontology (GO) terms in a list of microarray probe sets or gene identifiers (with expression information for PAGE analysis). Also EasyGO is also a GO annotation database, especially focus on agronomical species, supporting 30 species. It is user friendly, with advanced result browsing format and in-time update.

http://bioinformatics.cau.edu.cn/neweasygo/

http://bioinformatics.cau.edu.cn/easygo/

g:GOSt (Institute of Computer Science, University of Tartu)

g:GOSt retrieves most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs to a user-specified group of genes, proteins or microarray probes. g:GOSt also allows analysis of ranked or ordered lists of genes, visual browsing of GO graph structure, interactive visualisation of retrieved results, and many other features. Multiple testing corrections are applied to extract only statistically important results.

http://biit.cs.ut.ee/gprofiler/

DAVID : Gene Functional Classification (Laboratory of Immunopathogenesis and Bioinformatics, NIAID)

The Functional Classification Tool provides a rapid means to organize large lists of genes into functionally related groups to help unravel the biological content captured by high throughput technologies.

http://david.abcc.ncifcrf.gov/gene2gene.jsp

http://david.abcc.ncifcrf.gov/

API https://github.com/chrisamiller/davidapi

GOEAST (Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

GOEAST is web based software toolkit providing easy to use, visualizable, comprehensive and unbiased Gene Ontology (GO) analysis for high-throughput experimental results, especially for results from microarray hybridization experiments. The main function of GOEAST is to identify significantly enriched GO terms among give lists of genes using accurate statistical methods.

http://omicslab.genetics.ac.cn/GOEAST/

GOstat (Walter and Eliza Hall Institute of Medical Research)

Find statistically overrepresented GO terms within a group of genes

http://gostat.wehi.edu.au/

GOrilla (Technion - Laboratory of Computational Biology , Israel Institute of Technology)

GOrilla is a tool for identifying and visualizing enriched GO terms in ranked lists of genes.
It uses two approaches, first by searching for enriched GO terms that appear densely at the top of a ranked list of genes  or by searching for enriched GO terms in a target list of genes compared to a background list of genes.

GOrilla makes nice pictures !!!!

http://cbl-gorilla.cs.technion.ac.il/

Gene Ontology for Functional Analysis (GOFFA)

GOFFA is a tool developed for ArrayTrack™ that takes a list of genes and identifies terms in Gene Ontology (GO) disclaimer icon associated with those genes.

It provides several tools to view/access the GO term hierarchy, full listing of GO terms annotated with the genes associated with a given term with statically useful report.

http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm233315.htm

GOAT (The University of Manchester)

The aim of the GOAT project is to create an application that will guide users, especially biomedical researchers, in the annotation of gene products with terms from the Gene Ontology.

http://goat.man.ac.uk/

Script https://github.com/tanghaibao/goatools/

REVIGO ( Rudjer Boskovic Institute, Croatia)

REViGO is a web server that can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds.

http://revigo.irb.hr/

QuickGo (EMBL-EBI Institute)

It uses extensive computational filters to allow the generation of specific subsets of GO annotations, mapped to sequence identifiers of your choice. Then GO slims are used which is collective list of GO full set of terms available from the Gene Ontology project.

http://www.ebi.ac.uk/QuickGO/

GOLEM

An interactive graph-based gene-ontology navigation and analysis tool. GOLEM is a userful tool which allows the viewer to navigate and explore a local portion of the Gene Ontology (GO) hierarchy.

http://reducio.princeton.edu/GOLEM/

BGI Web Gene Ontology (WEGO) Annotation Plot (Beijing Genomics Institute)

WEGO () is a useful tool for plotting GO annotation results. It has been widely used in many important biological research projects, such as the rice genome project [Yu, J. et al. Science 296, 79-92 (2002); Yu, J. et al. PLoS Biol 3, e38 (2005)] and the silkworm genome project [Xia, Q. et al. Science 306, 1937-40 (2004)]. It has become one of the daily tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. WEGO along with two other tools, namely External to GO Query and GO Archive Query, are freely available for all users. Any suggestions are welcome at wego@genomics.org.cn. Here is a sample output generated by WEGO

http://wego.genomics.org.cn/cgi-bin/wego/index.pl

GeneGO MetaCore (MIT)

GeneGo is a leading provider of data mining & analysis solutions in systems biology. MetaCore, GeneGo's flapship product, is an integrated software suite for functional analysis of experimental data. MetaCore is based on a curated database of human protein-protein, protein-DNA interactions, transcription factors, signaling and metabolic pathways, disease and toxicity, and the effects of bioactive molecules.

https://portal.genego.com/

GOEx (Stony Brook University)

GOEx facilitates organism-specific studies by leveraging GO and providing a rich graphical user interface. It is a simple to use tool, specialized for biologists who wish to analyze spectral counting data from shotgun proteomics.

http://pcarvalho.com/patternlab

GOssTo

GOssTo and GOssToWeb are tools to calculate the semantic similarity between genes or terms in the Gene Ontology.

http://www.paccanarolab.org/gosstoweb/

GO Workbench

The Gene Ontology Analysis Viewer allows direct browsing of the Gene Ontology, and also the visualization of GO Term analysis results.

http://wiki.c2b2.columbia.edu/workbench/index.php/Gene_Ontology_Viewer

Some other useful list of GO software and tools is available at http://www.geneontology.org/GO.tools.shtml#browser

Yet another useful webpage with list of GO tools at http://neurolex.org/wiki/Category:Resource:Gene_Ontology_Tools

HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.

More at http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0678-x

Address of the bookmark: https://github.com/MWSchmid/HiCdat

Address of the bookmark: https://fuma.ctglab.nl/