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.
- 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.
- added reverse complement treatment for nucleotide sequences (plass nuclassemble)
--kmer-per-seq-scaleparameter 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 (
- add stdin support.
cat reads.fas | plass assemble stdin asm tmp
- reduced hard disk requirements by roughly a factor of 12 (
- 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
- overlaps are still sorted by ScorePerColumn but the bit score was replaced by the raw score to scale correctly with the overlap length
--min-contig-lenparameter 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
- 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
- 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.
- support to assemble on multiple compute using MPI
--min-lengthflag to adjust codon extraction length