vgan 3.1.0 - Fagiolo includes fixes for read mapping errors in all three subcommands. Please update all graph files with the new versions from our FTP server (description for each subcommand in the wiki).

vgan 3.1.0 now includes a standalone gam2prof command. It follows the same functionality as bam2prof for graph alignment files (game files). The manual can be called using vgan gam2prof

HaploCart had no changes but requires a re-download of its graph files for this version.

Additionally, we added a few new functionalities to euka and soibean.
euka:

1. --maxBins allows the user to adjust the number of bins required to have read mappings for the evenness of coverage estimation, making euka more sensitive.
2. -M option allows the use of alternative minimizes for mapping with vg giraffe
   soibean:
3. --alignment-detail will print out a tsv file with all alignments to each node ID
4. --pathThres In addition to the previous command, the user can define which alignments should be printed out, e.g. --pathThres 1 will print out only alignments that map to a signature node (show a unique variance for one of the paths present in the graph).
5. -M option allows the use of alternative minimizes for mapping with vg giraffe

Last, euka and soibean no longer require the data structure of the share/vgan/damageProfils. When ancient damage profiles are provided the likelihoods are adjusted, otherwise the default of ancient damage probability is set to 0.

This release includes "soibean", a tool designed for the species identification of a pre-analysed ancient environmental DNA sample.

• "soibean" identifies species, a mix of species as well as potential ancestral states of modern references from a FASTQ-file of reads that have been classified to a lower taxonomic resolution (e.g. family level)
• "soibean" uses an MCMC sampling algorithm to find the most likely position on a phylogenetic tree for a species or multiple closely related species in a given sample.
• At the current time, we are restricted to mitochondrial genomes from Tetrapoda and Arthropoda

Please note, if you would like to use euka with the new release, it is necessary to redownload euka's graph files as described in the README.

This release fixes minor mistakes in euka's likelihood function for classifying a read and the likelihood function used to compute the MCMC as well as corrections in the README.

This release includes "euka", a tool designed for the rapid and accurate characterization of ancient environmental DNA samples.

It uses a taxonomy-based pangenome graph of reference genomes for robustly assigning DNA sequences and uses a maximum-likelihood framework for abundance estimation.
At the present time, our database is restricted to mitochondrial genomes of tetrapods and arthropods but can be expanded in future versions.

This release includes "euka", a tool designed for the rapid and accurate characterization of ancient environmental DNA samples.

• It uses a taxonomy-based pangenome graph of reference genomes for robustly assigning DNA sequences and uses a maximum-likelihood framework for abundance estimation.
• At the present time, our database is restricted to mitochondrial genomes of tetrapods and arthropods but can be expanded in future versions.

Update to the Makefile to reflect changes in VG submodule dependencies.

In particular, the Makefile reverts commits of all VG submodules to avoid any future issues pertaining to changes to the VG codebase.

Minor fix to HaploCart help message and variable name (no change to the algorithm).

Make the static binary executable:
chmox +x vgan

Docker image: docker.io/gabrielreno/vganv1.0.0