metagenomics

installed only on cicuta

1. megahit

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

1. metabat2

version 2.12.1

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

1. prodigal

version 2.6.2

Fast, reliable protein-coding gene prediction for prokaryotic genomes.

1. pplacer

Phylogenetic placement and downstream analysis.

1. recycler

Recycler is a tool designed for extracting circular sequences from de novo assembly graphs. It can be applied on isolate as well as metagenome and plasmidome data. The circular sequences it outputs may be plasmids, phages, etc.

/opt/Recycler/bin/recycler.py

1. k-SLAM

k-SLAM ultra fast alignment and taxonomic classification of metagenomic datasets

SLAM

1. phyloFlash

phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an Illumina (meta)genomic or transcriptomic dataset.

perl /opt/phyloFlash-pf3.0b1/phyloFlash.pl -dbhome /mnt/databases/SILVA/