Parsnp v2.0.0

What's Changed

• You can now pass a newline-separated file of paths to query sequences to -d in addition to directories and command-line lists.
• Adds --partition flag, which splits recruited genomes into partitions of size --partition-size (default 50).
• Adds --no-recruit option which skips the recruitment step, but still drops genomes if their size differs substantially from the reference.
• Fixes multiple bugs in the output:
  • Output can now be parsed by BioPython's AlignIO module with the "mauve" format
  • LCBs no longer overlap
  • Ambiguous base pairs and small contigs no longer lead to incorrect coordinates
  • VCF now contains the correct reference allele.
• FastANI now guarantees at least 100 segments (unless it requires a fragment length < 500)
• Adds --min-ref-cov option (default 90), which when used with --use-ani, removes query genomes that do not cover at least 90% of the reference.
• Output folder has been reorganized to separate logs and config files from the main output.

Release v1.7.4

• abpoa and muscle have been replaced by mafft for inter-LCB alignment.

Release v1.7.3

The --extend-lcbs parameter now performs a gapped alignment using either muscle (>50nt) or abpoa (<=50nt) on inter-LCB regions. Alignments are trimmed back based on an ANI parameter that can also be provided by the user (i.e., cuts alignment off when it falls below 95% ANI). This parameter still only works w/ single contig genomes.

Also added better SeqIO validation. Throws out any genomes that can't be parsed.

Release v1.7.2

• Fix bug where Harvesttools is provided both a gbk and fasta reference.

v1.7.1

• Mismatch=-4 and gap=-2 for extending LCBs
• Fixed bug that created extra gaps in LCB extension
• Fixed bug that resulted in FastTree being used in cases when it wasn't requested
• Fixed bug that duplicated reference in alignment output
• Reference sequence is now first in extended xmfa output

Release v1.7.0

• Added option --extend-lcbs which uses a naive alignment to extend the boundaries of clusters.

Release v1.6.2

• No longer deletes the core SNPs file, parsnp.snps.mblocks. Users can now use that file to run their own custom phylogenetic analysis using this file as input.

Release v1.6.1

• Fixes an issue where a list was compared to an integer.

Release v1.6.0

• Add --skip-phylogeny option to allow users to skip phylogeny reconstruction
• Add --validate-input option to allow users to validate files provided by -d with Biopython parsing

Release v1.5.6

• Add option to generate .vcf output via the --vcf flag
• Remove tmp/ directory in output folder