Releases: polio-nanopore/piranha
piranha v1.4.2
piranha v1.4.1
Release notes
Additional references for WPV1 that represent consensus sequences from clusters of cases sequenced in 2024. This should help with mapping recent WPV1 sequences
piranha v1.4
Release notes
- New command line option:
-mo/--minimap2-options
This flag can be used to configure the mapping options to fine-tune the sensistivity of minimap2 for your data.
Specify one or more minimap2 command line options to overwrite the default mapping settings. The current default mapping configuration is set to -x asm20, however recent data has suggested for shorter read lengths there are sensitivity issues for samples diverged from the pre-installed reference set.
The options take the form flag=value and can be any number of space-delimited options.
Example:
Without any use of this flag, the command run in piranha for minimap2 is:
minimap2 -t [threads]
--secondary=no
--paf-no-hit
-x asm20
[ref] [reads] -o [outfile]
This command means that [threads] number of threads will be used, that only primary chains will be reported (the top hit for each read), and that in the output (PAF) file even reads with no hits will be recorded for record-keeping sake. The -x asm20 flag refers to the preset option to assemble a query against the entire target (our reads are longer than the reference, so this has worked well in simulations) and theoretically it should be able to handle up to 20% divergence.
With recent data and having recently being informed by Seedability, we are investigating changing the default settings for more sensitivity (perhaps in cases where few reads are mapping, or default accross the board).
For short reads of a sample diverged from the reference, we suggest using:
-mo k=5 w=4, which will overwrite the minimap2 option -x asm20 and result in the following minimap2 command being run:
minimap2 -t [threads]
--secondary=no
--paf-no-hit
-k5 -w4
[ref] [reads] -o [outfile]
which is a much smaller k (kmer) and w (minimiser window) size (5 and 4, as opposed to 19 and 10 with asm20). The default settings of minimap2 outwith piranha are k=15 and w=10, recommended for ONT data, however in the case of the DDNS protocol, read lengths are only ~1.2kb. According to Seedability, a much lower kmer and window size is appropriate.
Note: lowering the k and w values will increase the time taken for minimap2 to run.
Note: not all minimap2 options will be available for configuration as the output format must stay the same for piranha to reliably parse the output file (e.g. -a not available as it will produce a SAM file rather than a PAF file).
The options available within piranha for configuration are:
*** minimap2 configurable options within piranha ***
Options:
Indexing:
-k INT k-mer size (no larger than 28) [15]
-w INT minimizer window size [10]
Mapping:
-f FLOAT filter out top FLOAT fraction of repetitive minimizers [0.0002]
-g NUM stop chain enlongation if there are no minimizers in INT-bp [5000]
-G NUM max intron length (effective with -xsplice; changing -r) [200k]
-F NUM max fragment length (effective with -xsr or in the fragment mode) [800]
-r NUM bandwidth used in chaining and DP-based alignment [500]
-n INT minimal number of minimizers on a chain [3]
-m INT minimal chaining score (matching bases minus log gap penalty) [40]
Alignment:
-A INT matching score [2]
-B INT mismatch penalty [4]
-O INT[,INT] gap open penalty [4,24]
-E INT[,INT] gap extension penalty; a k-long gap costs min{O1+k*E1,O2+k*E2} [2,1]
-z INT[,INT] Z-drop score and inversion Z-drop score [400,200]
-s INT minimal peak DP alignment score [80]
-u CHAR how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]
Preset:
-x STR preset (always applied before other options; see minimap2.1 for details) []
- map-pb/map-ont: PacBio/Nanopore vs reference mapping
- ava-pb/ava-ont: PacBio/Nanopore read overlap
- asm5/asm10/asm20: asm-to-ref mapping, for ~0.1/1/5% sequence divergence
- splice: long-read spliced alignment
- sr: genomic short-read mapping
- fixing space in path issue within piranha, still issue for no-temp within medaka itself
- adding a read-length log for preprocessing step, it seems read length is a piece of info not being fully documented prior to analysis with piranha. can build on this commit with a histogram of some sort for read lengths
- overwrite readdir input with the dir you actually find the reads in within that
- check for no barcodes found, break and exit with error if that's the case
piranha v1.3.1
Release notes
- Some minor updates, including handling special case of argument when entry value is 0, making sure it is applied to the configuration. Issue #247
- Recursively search the directory tree for FASTQ files, check if the parent directory is barcodeXX, catalogue barcode dirs found and overwrite input path with the path to barcode dirs if it is not already the same. Issue #186
- Issue #178 resolved, in config table now
piranha v1.3
Release notes
- Merge in updates from wt-dev branch
- Split reference mapping now choose best score hit, rather than filtering out as ambiguous
- whole genome and pan-ev pipelines removed, now just selects different reference panels
- Masking for low-coverage implemented as a post-hoc processing step informed by information from the pileup
- Docker image updated to cope with tensorflow incompatibility issues
piranha v1.2.5
Bump for tensorflow version pin in Docker image, but to 1.10 this time
piranha v1.2.4
Bumped release to try fix Docker build issues (medaka related).
piranha v1.2.3
- Updated tag for piranha main
- Now contains reference group as a tag
piranha v1.2.2
Release notes
- Update config.py for issue #187
- Removing the new references added that conflict with ones already there for pos control
piranha v1.2.1
Release notes
- Update to phylo, patch for no supp datadir provided.
- Flag for parameter name for phylo in Epi2Me updated
- Demo updated to reflect change to phylo