Tigmint Versions Save

• Release Tigmint v1.2.10
• Allow fastq.gz and fasta.gz input read formats
• Dockerfile fix
• Update documentation

• Release Tigmint v1.2.9
• Use sensitive=True option for ntLink mapping (#113)

• Release Tigmint v1.2.8
• When mapping=ntLink is added to the tigmint-make command, use ntLink for mapping long reads to the draft assembly instead of minimap2 (#110)
  • This ntLink mapping approach doesn't split the long reads into pseudo-linked reads
• Add option to use memusg for benchmarking the pipeline (if found in PATH) (#110)
• Bugfix to tigmint-cut (#110)
• Benchmarking fix (#109)

• Release Tigmint v1.2.7
• Remove packaged btllib, making it a dependency
• Documentation fixes

• Release Tigmint v1.2.6
• In long-read mode, Tigmint (Tigmint-long) now accepts long read files in fa or fq formats, gzipped or uncompressed (.fa, .fa.gz, .fq., .fq.gz
• Update btllib to v1.4.1
• Add SORT_OPTS parameter for specifying additional parameters for sort
• Bugfixes
• Documentation improvements

• Updated tigmint-make file to include tigmint steps as targets, such as tigmint-index (perform the bwa index step)
• Updated tigmint-make to include dist parameter in naming convention of output files

• Changed the default value for genome size parameter: now G=0 if unset
• Added extra checks for G to be set if using span=auto in tigmint-make

• Release version 1.2.3
• Added tigmint_molecule_paf.py for inferring molecule extents from minimap2 paf mappings (tigmint-long)
• Added tigmint_estimate_dist.py to estimate the dist parameter from the first 1M reads (tigmint-long)
• Translated long-to-linked-pe script to C++ (thanks @jowong4)
• Documentation updates
• Bugfixes

This version of Tigmint includes a couple of changes to the tigmint-long option:

• long-to-linked produces a fastq file of cut long reads instead of fasta
• the dist parameter is calculated automatically based on the distribution of long read lengths

Tigmint Version 1.2.1

This version corrects a bug introduced in version 1.2.0. The bug affected barcode assignment during long read processing, which then prevented proper corrections.