I want to perform a multi-sequence alignment on 12 samples that clustered based on cgMLST. Ultimate goal is to find out whether they differ by the presence of a few genes.
I have performed multi-sequence alignment in the past using MAFFT, the main difference being that, back then, I was aligning protein sequences, and now I want to align multiple denovo assembled genomes, with multiple contigs each
I first had a look at MAFFT, the program that I used in the past for protein multi-sequence alignment, though I noticed that it considers each contig in a denovo assembly as independent sequence, which is not what I want
Then I had a look at Mauve, but was discouraged by installation trouble-shooting. Also I read on their webpage:
When an individual file contains several sequence entries, they will be concatenated and the whole concatenated sequence will be aligned to the sequences in the other files. This behavior allows multi-chromosomal genomes to be aligned by including all chromosomes in a single sequence file. Similarly, incomplete genomes that consist of several sequence contigs can be aligned, though beware that incorrectly ordered contigs will appear as genome rearrangements in the Mauve viewer.
So I guess concatenating all contigs in a single fasta file is not an option, as artefacts (genome rearrangements) might appear
It turns out that MAFFT has also an experimental feature to multi-align fastq reads, which sounds attractive to me. Therefore I would like to ask if anyone can recommend this new/ experimental feature. Also if this option is available on the command-line tool, as the mafft help is quite limited (it does not specify the format of input and output files):
MAFFT v7.505 (2022/Apr/10) https://mafft.cbrc.jp/alignment/software/ MBE 30:772-780 (2013), NAR 30:3059-3066 (2002) ------------------------------------------------------------------------------ High speed: % mafft in > out % mafft --retree 1 in > out (fast) High accuracy (for <~200 sequences x <~2,000 aa/nt): % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok) % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out) % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out) If unsure which option to use: % mafft --auto in > out --op # : Gap opening penalty, default: 1.53 --ep # : Offset (works like gap extension penalty), default: 0.0 --maxiterate # : Maximum number of iterative refinement, default: 0 --clustalout : Output: clustal format, default: fasta --reorder : Outorder: aligned, default: input order --quiet : Do not report progress --thread # : Number of threads (if unsure, --thread -1) --dash : Add structural information (Rozewicki et al, submitted)
Any other recommendation on another strategy to align multiple denovo assembled genomes with multiple contigs each are welcome