Full command-line help for `myloasm`

myloasm - high-resolution metagenomic assembly with noisy long reads. See online documentation for full options.

EXAMPLE (Nanopore R10): myloasm nanopore_reads.fq.gz -o output_directory -t 50

EXAMPLE (PacBio HiFi): myloasm pacbio_reads.fq.gz -o output_directory -t 50 --hifi

Usage: myloasm [OPTIONS] <FASTQ/FASTA (.gz)>...

-c, --c <C> — Compression ratio (1/c k-mers selected). Must be <= 15 [11]
--quality-value-cutoff <QUALITY_VALUE_CUTOFF> — Disallow reads with < % identity for graph building (estimated from base qualities) [90]
--min-ol <MIN_OL> — Minimum overlap length for graph construction [500]
-b, --bloom-filter-size <BLOOM_FILTER_SIZE> — Bloom filter size in GB. Increase for massive datasets [10]
--aggressive-bloom — More aggressive filtering of low-abundance k-mers. May be non-deterministic
-k, --kmer-size <KMER_SIZE> — K-mer size (must be odd and < 24) [21]

--nano-r10 — (DEFAULT) R10 nanopore mode for sup/hac data (> ~97% median accuracy). Specifying this flag does not do anything for now
--nano-r9 — R9 (old nanopore) mode for low (~90%) accuracy reads. Experimental
--hifi — PacBio HiFi mode -- assumes less chimericism and higher accuracy

--min-reads-contig <MIN_READS_CONTIG> — Output contigs with >= this number of reads [1]
--singleton-coverage-threshold <SINGLETON_COVERAGE_THRESHOLD> — Remove singleton contigs with <= this estimated coverage depth (DP1 coverage; 99% identity coverage) [3]
--secondary-coverage-threshold <SECONDARY_COVERAGE_THRESHOLD> — Remove contigs with <= this estimated coverage depth and <= 2 reads (DP1 coverage; 99% identity coverage) [1]
--absolute-coverage-threshold <ABSOLUTE_COVERAGE_THRESHOLD> — Remove all contigs with <= this estimated coverage depth (DP1 coverage; 99% identity coverage)

--small-bubble-threshold <SMALL_BUBBLE_THRESHOLD> — Base bubble popping length threshold; this gets multiplied by 5-30x during progressive graph cleaning [50000]
--z-edge-threshold <Z_EDGE_THRESHOLD> — Cut z-edges that are < this times smaller than the adjacent overlaps [1]
--tip-length-cutoff <TIP_LENGTH_CUTOFF> — Base length of tip to remove; this gets multiplied by 5-30x during simplification [20000]
--tip-read-cutoff <TIP_READ_CUTOFF> — Number of reads in tips to remove; this gets multiplied by 5-30x during simplification [3]
--max-bubble-threshold <MAX_BUBBLE_THRESHOLD> — Maximum bubble length to pop; keep alternates [500000]

-o, --output-dir <OUTPUT_DIR> — Output directory for results; created if it does not exist [myloasm-out]
-t, --threads <THREADS> — Number of threads to use for processing [20]
--clean-dir — Do not dump large intermediate data to disk (intermediate data is useful for rerunning)
-l, --log-level <LOG_LEVEL> — Verbosity level. Warning: trace is very verbose [debug]

Possible values: error, warn, info, debug, trace

--read-map-batch-size <READ_MAP_BATCH_SIZE> — Batch size of indexing for read-to-read mapping and overlap stage [1000000]
--snpmer-threshold-strict <SNPMER_THRESHOLD_STRICT> — Snpmer identity threshold for containment and strict overlaps [100]
--snpmer-threshold-lax <SNPMER_THRESHOLD_LAX> — Snpmer identity threshold for relaxed overlaps [99]
--snpmer-error-rate-lax <SNPMER_ERROR_RATE_LAX> — Binomial test error parameter for relaxed overlaps [0.025]
--snpmer-error-rate-strict <SNPMER_ERROR_RATE_STRICT> — Binomial test error parameter strict overlaps [0]
--contain-subsample-rate <CONTAIN_SUBSAMPLE_RATE> — Relaxed compression ratio during containment; must be > c [44]
--absolute-minimizer-cut-ratio <ABSOLUTE_MINIMIZER_CUT_RATIO> — Cut overlaps with > (c * this) number of bases between minimizers on average [8]
--relative-minimizer-cut-ratio <RELATIVE_MINIMIZER_CUT_RATIO> — Cut overlaps with > (this) times more bases between minimizers than the best overlap on average [5]
--disable-error-overlap-rescue — Disables a SNPmer error overlap rescue heuristic during graph construction
--maximal-end-fuzz <MAXIMAL_END_FUZZ> — Soft clips with < this # of bases are allowed for alignment [300]

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Full command-line help for myloasm