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  • 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
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  • 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
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  • 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
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  • 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
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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
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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.

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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
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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.

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  • 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