Plass & Penguin Release Notes

First release of Penguin, a metagenomic assembler that assembles DNA/RNA through a novel greedy AA/DNA-hybrid bayesian overlap extension strategy.

New Features and Enhancements

• First release of Penguin: We generate now two binaries, plass and penguin. Plass assembles protein sequences from DNA while Penguin assembles DNA contigs. Penguin comes in two variants penguin guided_nuclassemble, which first assembles using AA six-framed-translated overlaps and then further assemble the contigs using nucleotide information and a pure nucleotide assembler penguin nuclassemble.
• Compatibility and Portability: Thanks to simde Plass and Penguin now run on ARM (including Apple Silicon) and POWERPC.

Changes since Release 3-764a3:

At a glance: Significant further development of the nucleotide/hybrid assembler. Updated MMseqs2 submodule and adjusted Plass to multiple MMseqs2 changes.

Features

• Plass can extend one contig multiple times within one iteration
• Hybrid assembly is progressing nicely, stay tuned for updated!
• Plass works on many more architectures (e.g. PPC64LE, ARM64 and x64 with SSE2 only)

Changes since Release 2-c7e35:

At a glance: Significant further development of the nucleotide assembler. Reduced hard disk requirements for protein assembler and many bug fixes.

Updated mmseqs submodule and adjusted plass to multiple MMseqs2 changes.

Breaking Changes

• added reverse complement treatment for nucleotide sequences (plass nuclassemble)
• introduced --kmer-per-seq-scale parameter to make sure not to miss good hits of long sequences. The number of extracted kmers can now be scaled with a user defined factor multiplied by the length of the sequence.
• changed scoring mode for alignment calculation (--rescore-mode 3)

Features

• add stdin support. cat reads.fas | plass assemble stdin asm tmp
• reduced hard disk requirements by roughly a factor of 12 (--delete-tmp-inc)
• added a first raw version of a cycle detector (still experimental) to avoid over extension for nucleotide assembly
• introduced a new header format, which is now consistent for protein and nucleotide assembler <uniq ID> len:<len> cycle:<0|1> The cycle field is optional (for the nucleotide case)
• introduced a new logic to handle sequences with N repeated k-mers: sequences with more than N repeated k-mers are no longer ignored in the assembly process completely, but instead repeated k-mers are only ignored in the kmermatcher phase. Replaced --skip-n-repeat parameter by --ignore-multi-kmer
• overlaps are still sorted by ScorePerColumn but the bit score was replaced by the raw score to scale correctly with the overlap length
• introduced --min-contig-len parameter to set minimum length of assembled contig to output (for nucleotide assembly)
• added redundancy reduction (for nucleotide assembly) by clustering sequences based on user defined threshold (--clust-thr, default 0.97)
• Dockerfile now uses Debian slim instead of alpine

Bugs

• fixed problems in the first iteration of the protein assembler
• fixed problems with start and stop codons occurring in the transition from protein alignments to nucleotide alignments and alignment offset calculation
• split file existence check in workflows to individual checks to avoid repeated linking problems
• fixed bug in the reverse complement calculation for N's in nucleotide sequences
• fixed different problems for long sequences regarding the kmermatching phase
• fixed broken compilation without zlib

Changes since release 1-2e0ef

• overlaps are now sorted by score per column instead of sequence identity
• new flag to change neural network threshold of filtering proteins --protein-filter-threshold
• improve neural network by retraining with cleaner training data
• add support to merge paired-end files with different length
• fix a bug in start codon correction

Plass Release 1-2e0ef

Plass (Protein-Level ASSembler) is a software to assemble short read sequencing data on a protein level. The main purpose of Plass is the assembly of complex metagenomic datasets.

Features

• support to assemble on multiple compute using MPI
• Add --min-length flag to adjust codon extraction length

First Plass release