Tigmint Version 1.2.0

This version expands the functionality of Tigmint by allowing the use of long sequencing reads as input for the pipeline. Long reads are segmented and aligned to the draft assembly with Minimap2 instead of BWA-MEM. Long reads can be provided in either FASTA or FASTQ format.

• tigmint-make: the target tigmint-long runs the Tigmint pipeline with long reads
• long-to-linked: this script cuts the long reads and optionally calculates the optimal span parameter for the reads based on their sequence coverage
• tigmint-cut: the option -s was added to read in the span parameter calculated by long-to-linked

Version 1.1.2 corrects a bug introduced in version 1.1.0. Multiple molecules with the same barcode found on the same contig were not output.

• Version 1.1.1 corrects a significant bug present in version 1.1.0. The molecule BED file was not sorted, which rendered the tool non-fuctional for assemblies with more than one contig.
• tigmint-make: ARCS can use the BX:Z SAM tag and no longer needs the barcode in the read ID
• tigmint-molecule: Add the option -s, --size to specify a minimum molecule size