LRSDAY v1.7.2

[1.7.2] - 2023-03-20

Changed

• Better support for historical PacBio RSII reads.
• Cleaner TE output in the final annotation GFF3 file.

LRSDAY v1.7.1

[1.7.1] - 2023-01-28
Fixed

A bug leading to the loss of detailed TE subtype info in the final annotation GFF3 file.

LRSDAY v1.7.0

[1.7.0] - 2022-12-31

Changed

• Better robunsteness for the dependency installation script.
• Functional enhancement for the basecalling, demultiplexing, and quality summary of ONT raw fast5 reads.
• Version updates for multiple genome assemblers.
• Functional enhancement for the mitochondrial genome assembly.
• Functional enhancement for the mitochondrial gene annotation.
• Functional enhancement for the nuclear gene annotation.
• Functional enhancement for the TE annotation.
• Functional enhancement for SGD_based orthology identification and tagging.
• Removal of support for the long-read-assembler: Ra.
• Removal of support for the long-read-polisher: MarginPolish.

LRSDAY v1.6.0

[1.6.0] - 2019-10-03

Added

• Supports for canu-triobinning assembly mode for phased diploid genome assembly.
• Supports for new alternative long-read-assemblers: Ra and Shasta.
• Supports for new alternative long-read-based polishers: Racon, Medaka, and MarginPolish.
• Supports for new alternative reference-genome-based scaffolder: RaGOO.

Changed

• Better robustness for the dependency installation script.
• Better treatment for identifying mitochondrial contigs when they contain assembly gaps.
• Minor adjustment for a few task-specific directory names.
• Software version updates for a number of dependencies.

Fixed

• A bug that will disrupt long-read-based assembly run when assembler="canu-flye", "canu-wtdbg2" or "canu-smartdenovo" because of deleting a non-existing file.

LRSDAY v1.5.0

[1.5.0] - 2019-05-13

Added

• Supports for native ONT nanopore basecalling, demultiplexing, and read profile plotting.
• An lite-weight bash script for generating dotplot for any pairs of fasta files.

Changed

• Better robustness for the dependency installation script.
• Reducing the requirements of setting output prefix by assuming the same prefix was used across different modules.
• Setting adjustment for long-read filtering and downsampling.
• Applying read filtering/downsampling for the testing example.
• Software version updates for a number of dependencies.

Fixed

• A bug that might lead to missing gene annotation in certain genomic region.
• Typos in the installation script.
• Typos in the manual.

LRSDAY v1.4.0

[1.4.0] - 2019-03-21

Changed

• Supports for multi-round assembly polishing using both long and short reads.
• Setting adjustment for long-read filtering and downsampling.
• Software version updates for a number of dependencies.

Fixed

• Compatibility issues due to recent version updates of conda an bioconda.
• Typos in the installation script.

LRSDAY v1.3.1

[1.3.1] - 2019-01-22

Added

• A script for generated demultiplexed fastq reads based on nanopore's guppy demultiplexing summary file.
• A script for extracting all read IDs from the input fastq file.
• A script for calculating the sequence length of each enclosed sequences from the input fasta file.

Changed

• Software version updates for a number of dependencies. Importantly, nanopolish was bumped up to v0.11.0 to support the new multi-fast5 nanopore reads.
• Downloading URL updates for testing data due to changes on the EBI data server.
• Adopting picard tools' new commandline syntax.

Fixed

• A bug that prevents correct parameter parsing when multiple customized canu parameters are specified.
• Minor bugs related with deleting intermediate files in special cases.

LRSDAY v1.3.0

[1.3.0] - 2018-11-13

Added

• Support for one more alternative assembler: wtdbg2.

Changed

• Substantially more automated installation/setup process.
• Software version or downloading URL updates for a number of dependencies.

Fixed

• Bugs introduced due to changes made for file/parameter names in the LRSDAY.01.Long-read-based_Genome_Assembly.sh script when using some alternative assemblers.
• Mismatched step numbers and file names in the manual due to previous version changes.
• Typos in the manual.

LRSDAY v1.2.0

[1.2.0] - 2018-10-15

Added

• Support for adapter trimming for Nanopore reads (via Porechop).
• Support for long-read filtering based on both quality and length (via Filtlong).
• Support for long-read-based polishing for PacBio and Nanopore reads (via Quiver/Arrow for PacBio reads and nanopolish for Nanopore reads).
• Support for the bax2bam format conversion for the PacBio RSII reads to make it compatible with PacBio's current SMRT pipeline.
• Support for dedicated mitochondrial gene annotation (via Mfannot).

Changed

• Treat nuclear genome and mitochondrial genome separately in the annotation phase.
• Better robustness for various processing scripts.
• Software version or downloading URL updates for a number of dependencies.

Fixed

• Typos in the manual.

LRSDAY v1.1.0

[1.1.0] - 2018-07-11

Added

• This change log file: Changelog.md
• Support for customized parameter settings for Canu.
• Support for alternative assemblers: Flye and smartdenovo.
• The script subsampling_seqeunces.pl for downsampling input reads.
• Support for the report of exact numbers of SNP and INDEL corrections made based on the Illumina data.

Changed

• Better resource management for the Illumina-based polishing step.
• Better robustness for the reference-based scaffolding step.
• Better performance and robustness for the mitochondrial genome assembly improvement step.
• Better robustness for the TE annotation step.
• Better robustness for the reference-based gene orthology identification step.
• Software version or downloading URL updates for a number of dependencies.
• Preparation for future incorporation of long-read-based polishing step.

Fixed

• A bug in the script identify_contigs_for_RefChr_by_mummer.pl that ignores user-specified options.
• Typos in the manual.