| name | plass |
| description | PLASS — protein-level assembler that recovers many more protein sequences from metagenomic reads than nucleotide assembly alone (Söding / Steinegger). Same package ships PenguiN (protein-guided nucleotide assembly). Use when: (1) Maximizing protein catalogue recovery from reads, (2) Building inputs for MMseqs/HH-suite/BFD-style search, (3) Viral/strain-resolved assemblies via PenguiN. Upstream: https://github.com/soedinglab/plass. Route via homology-search / assembly stages.
|
| license | MIT |
| category | analysis-tools |
| tags | ["PLASS","PenguiN","assembly","protein","metagenomics"] |
| upstream | https://github.com/soedinglab/plass |
| stage | assembly |
PLASS / PenguiN
Upstream: soedinglab/plass
Citation
Steinegger, M., Mirdita, M. & Söding, J. Protein-level assembly increases
protein sequence recovery from metagenomic samples manyfold. Nat. Methods
16, 603–606 (2019). https://doi.org/10.1038/s41592-019-0437-4
Jochheim, A. et al. Strain-resolved de-novo metagenomic assembly of viral
genomes and microbial 16S rRNAs. Microbiome 12, 187 (2024).
https://doi.org/10.1186/s40168-024-01904-y
See also docs/references.md.
Analytical thinking
Nucleotide assemblers miss many coding sequences. PLASS assembles at the
protein level from reads → denser protein catalogues for search/annotation.
PenguiN uses protein guidance for nucleotide assemblies (viruses/16S use
cases in the paper). Complements MEGAHIT/metaSPAdes, does not replace contig
binning paths.
Soil/Marine reference catalogues from PLASS and BFD HH-suite DBs are linked
from upstream.
How to run
conda install -c bioconda plass
plass assemble reads_1.fastq.gz reads_2.fastq.gz assembly.fas tmp
plass assemble reads.fastq.gz assembly.fas tmp
Decision tree
Goal from metagenomic reads?
├─ Contigs for binning → megahit / metaspades
├─ Maximize protein recovery for search → plass
├─ Protein-guided nt assembly (viruses/…) → penguin (plass package)
└─ Then search proteins → mmseqs2 / hh-suite / foldseek
Related skills
megahit · metaspades · mmseqs2 · hh-suite · homology-search ·
prodigal · tool-selection
