Run integrated SKESA on reads from each cell.
Usage
BascetMapCellSKESA(
bascetRoot,
inputName = "filtered",
outputName = "contigs",
numThreads = NULL,
numSkesaWorkers = NULL,
numSkesaCores = NULL,
numThreadsRead = NULL,
totalMem = NULL,
kmer = 21,
maxKmer = 0,
steps = 11,
minCount = NULL,
maxKmerCount = 10,
vectorPercent = 0.05,
insertSize = 0,
fraction = 0.1,
maxSnpLen = 150,
minContig = 50,
allowSnps = FALSE,
forceSingleEnds = FALSE,
singlePassCounter = FALSE,
maxReadsPerCell = 0,
overwrite = FALSE,
runner = GetDefaultBascetRunner(),
bascetInstance = GetDefaultBascetInstance()
)Arguments
- bascetRoot
The root folder where all Bascets are stored
- inputName
Name of input shard
- outputName
Name of output shard
- numThreads
Total thread budget. Defaults to the runner CPU count
- numSkesaWorkers
(Advanced) Number of cells to assemble concurrently
- numSkesaCores
(Advanced) Number of cores to give each SKESA assembly
- numThreadsRead
(Advanced) Threads used by the TIRP reader. If NULL, use the CLI default
- totalMem
Total memory to allocate
- kmer
Minimal k-mer length for assembly
- maxKmer
Maximal k-mer length for assembly. 0 means auto
- steps
Number of assembly iterations from minimal to maximal k-mer length
- minCount
Minimal count for k-mers retained. NULL (default) lets skesa auto-estimate it from coverage, raising it for high-coverage cells
- maxKmerCount
Maximum k-mer count for fork tie-breaking
- vectorPercent
Percentage of reads containing 19-mer for adapter detection. 1.0 disables
- insertSize
Expected insert size for paired reads. 0 means auto
- fraction
Maximum noise to signal ratio acceptable for extension
- maxSnpLen
Maximal SNP length
- minContig
Minimal contig length reported in output
- allowSnps
Allow additional step for SNP discovery
- forceSingleEnds
Do not use paired-end information
- singlePassCounter
Use the legacy single-pass k-mer counter. Faster for small cells but can exceed the memory budget for high-coverage cells, so it is off by default
- maxReadsPerCell
Maximum read pairs per cell fed to assembly. 0 (default) disables the cap. When a cell exceeds this, only the first N read pairs encountered in the file are used (no random subsampling). Bounds memory for pathological high-read cells
- overwrite
Force overwriting of existing files. The default is to do nothing files exist
- runner
The job manager, specifying how the command will be run (e.g. locally, or via SLURM)
- bascetInstance
A Bascet instance