Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multi...rxiv.org/pdf/1902.04341.pdf More at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bio...1537 days ago
JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. https://github.com/tanghaibao/jcvi More at https://github.com/tanghaibao/jcvi/wiki1537 days ago
QuartataWeb: user-friendly server developed for polypharmacological and chemogenomics analyses.
Data on protein-drug and protein-chemical interactions are rapidly accumulating in databases such as DrugB...cals, or polypharmacological treatments. https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bio...1521 days ago
Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
...ows including data pre-processing, metagenome assembly, taxonomic and functional classification, genome binning, a...n, and execution problems typically associated with other open-source bioinformatics solutions. This wi...1514 days ago
PPAI: a web server for predicting protein-aptamer interactions
PPAI can query aptamers and proteins, predict aptamers and predict protein-aptamer interactions in batch mode precisely and efficiently, which would be a novel bioinformatics tool for the research of protein-aptamer interactions. PPAI web-server is freely available at http://39.96.85.9/PPAI1450 days ago
ShinyGO v0.61: Gene Ontology Enrichment Analysis + more
2/3/2020: Now published by Bioinformatics. 11/3/2019: V 0.61, Improve graphical visu...base updated to Ensembl 96. New bacterial and fungal genomes based on STRING-db...ditional 2031 genomes (including bacteria and fungi) are annotated based on STR...1459 days ago
PhiSpy: PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes
PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated...Sajia Akhter (sajia@stanford.edu) Edwards Bioinformatics Lab Improvements, bug fixes,...hanges were made by Katelyn McNair Edwards Bio...1431 days ago
wgd—simple command line tools for the analysis of ancient whole-genome duplications
wgd is a easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides common...ble to genomics researchers in a convenient manner. https://academic.oup.com/bio...1409 days ago
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
SHAMAN is a shiny application for differential analysis of metagenomic data (16..., 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for ta...t, boxplot, heatmap, …).The bioinformatics treatment is based on Vsearch...re. More at https://bmcbio...1384 days ago
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