Bakta: rapid & standardized annotation of bacterial genomes, MAGs & plasmids Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis. Description Comprehensive & taxonomy-independent database Bakta provides a large and taxonomy-independent database using UniProt’s entire UniRef protein sequence cluster universe.

GoSTRIPES: Computational workflows for STRIPE-seq data analyses The GoSTRIPES repository encompasses code and scripts developed in the Brendel and Zentner groups for analyses of STRIPE-seq data. The code conforms to our RAMOSE philosophy: it generates reproducible, accurate, and meaningful results; it is open (source) and designed to be scalable and easy to use. Quick Start All the GoSTRIPE dependencies are encapsulated in a Singularity container available from Singularity Hub. Thus, once you know what you are doing, execution could be as simple as

What is Salmon? Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves its accuracy and speed via a number of different innovations, including the use of selective-alignment (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many different pipelines. For example, you can choose to make use of our selective-alignment algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.

TransDecoder (Find Coding Regions Within Transcripts) TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. TransDecoder identifies likely coding sequences based on the following criteria: a minimum length open reading frame (ORF) is found in a transcript sequence a log-likelihood score similar to what is computed by the GeneID software is > 0.

Trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.

MetaPhlAn: Metagenomic Phylogenetic Analysis What’s new in version 3 New MetaPhlAn marker genes extracted with a newer version of ChocoPhlAn based on UniRef Estimation of metagenome composed by unknown microbes with parameter --unknown_estimation Automatic retrieval and installation of the latest MetaPhlAn database with parameter --index latest Virus profiling with --add_viruses Calculation of metagenome size for improved estimation of reads mapped to a given clade Inclusion of NCBI taxonomy ID in the ouput file CAMI (Taxonomic) Profiling Output Format included Removal of reads with low MAPQ values ————- Description MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.