Version 1.3.0

Updated SNP calling

• Core-genome SNPs are determined based on pooling data across multiple samples
• SNPs are now reference-independent: the major and minor alleles are determined from aligned reads
• Added presets for commonly used sets of parameters: --core-snps, --core-sites, --all-snps, --all-sites
• Improved speed and parallelization
• Switched from global to local Bowtie2 read alignment; alignment coverage can be specified using the --aln_cov option

Updated DB building code

• Switched from USEARCH to VSEARCH
• Added function to write genome_info.txt file (issue #60 )

Updated binaries

• Bowtie2 (2.3.2) and Samtools (1.4) updated
• Allows for interleaved reads and improved parallelization

Updated documentation

• Added use cases for snp_diversity.py (issue #61 )

Bug fixes

• Fixed bug in run_midas.py snps (issue #57 )
• Test suite updated (issue #56 )
• Updated snp_diversity.py includeing bug fixes (issue #53 )