Conda See the ‘activating the conda environment’ section below to access this software. trinity-2.13.2 RNA-Seq De novo Assembly Using Trinity Quick Guide for the Impatient Trinity assembles transcript sequences from Illumina RNA-Seq data. Assemble RNA-Seq data like so: Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU 6 --max_memory 20G Find assembled transcripts as: ‘trinity_out_dir/Trinity.fasta’ Use the documentation links in the right-sidebar to navigate this documentation, and contact our Google group for technical support.

Conda See the ‘activating the conda environment’ section below to access this software. vechat-1.1.1 Correcting Errors in Noisy Long Reads Using Variation Graphs Description Error correction is the canonical first step in long-read sequencing data analysis. The current standard is to make use of a consensus sequence as a template. However, in mixed samples, such as metagenomes or organisms of higher ploidy, consensus induced biases can mask true variants affecting haplotypes of lower frequencies, because they are mistaken as errors.

Conda See the ‘activating the conda environment’ section below to access this software. CONSENT-2.2.2 CONSENT (Scalable long read self-correction and assembly polishing with multiple sequence alignment) is a self-correction method for long reads. It works by, first, computing overlaps between the long reads, in order to define an alignment pile (i.e. a set of overlapping reads used for correction) for each read. Each read’s alignment pile is then further divided into smaller windows, that are corrected idependently.

Conda See the ‘activating the conda environment’ section below to access this software. Bakta 1.5.1: 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.

Installed This software should be available with no extra configuration. itsxpress-1.8.0 The internally transcribed spacer region is a region between highly conserved the small subunit (SSU) of rRNA and the large subunit (LSU) of the rRNA. In Eukaryotes it contains the 5.8s genes and two variable length spacer regions. In amplicon sequencing studies it is common practice to trim off the conserved (SSU, 5,8S or LSU) regions. Bengtsson-Palme et al.

Installed This software should be available with no extra configuration. vsearch-2.22.1 The aim of this project is to create an alternative to the USEARCH tool developed by Robert C. Edgar (2010). The new tool should: have open source code with an appropriate open source license be free of charge, gratis have a 64-bit design that handles very large databases and much more than 4GB of memory be as accurate or more accurate than usearch be as fast or faster than usearch We have implemented a tool called VSEARCH which supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting.