Print query names to stderr, mostly to see which query is crashing minimap2. Minimap2 runs slower with this option, especially in the This debugging option is mostly used with Valgrind to detect invalid memoryĪccesses. Use the libc default allocator instead of the kalloc thread-local allocator. Oxford Nanopore all-vs-all overlap mapping Long-read splice alignment for PacBio CCS reads ms tag ignores introns to demote hits to pseudogenes. N CIGAR operator 2) long insertions are disabled 3) deletion and insertion gapĬosts are different during chaining 4) the computation of the In the splice mode, 1) long deletions are taken as introns and represented as Only use this preset if the average divergence is far below 5%. Typically, the alignment will not extend to regions with 5% or higher sequenceĭivergence. This is theĪlign PacBio high-fidelity (HiFi) reads to a reference genome It should beĪpplied before other options because options applied later will overwrite theĪlign noisy long reads of ~10% error rate to a reference genome. This option applies multiple options at the same time. Warning: some paftools.js commands may not work with such output In PAF, output unmapped queries the strand and the reference name fields are NUM helps load balancing in the multi-threading mode, at the cost of increased Number of bases loaded into memory to process in a mini-batch. Apply this option to use one thread for inputĪnd another thread for output, at the cost of increased peak RAM. piping to gzip, or reading from a slow pipe), the I/O By default, minimap2 uses one I/O thread. INT+1 threads when mapping (the extra thread is for I/O, which is frequently idle and Minimap2 uses at most three threads when indexing target INT and read name when choosing between equally best hits. Integer seed for randomizing equally best hits. In SAM output, use soft clipping for supplementary alignments. Output =/X CIGAR operators for sequence match/mismatch. In PAF, the CIGAR is written to the cg custom tag. Newer tools recognizes this tag and reconstruct This option makes minimap2 SAMĬompatible with older tools. Older tools are unable toĬonvert alignments with >65535 CIGAR ops to BAM. NUM2 for RMQ-based re-chaining and closing gaps in alignments.Ħ5535 operators at the CG tag. NUM1 is used for initial chaining and alignment extension Stop chain enlongation if there are no minimizers withinīandwidth for chaining and base alignment. min-occ-floor in earlier versions of minimap2.ĭiscard a query minimizer if its occurrence is higher thanįLOAT fraction of query minimizers and than the reference occurrence threshold This option prevents excessively small or large Lower and upper bounds of k-mer occurrences. xsr mode, which sets the threshold for a second round of seeding. Mapping options -f FLOAT | INT1 įLOAT fraction of most frequent minimizers. H, -k, -w, -I will be effectively overridden by the options stored in the index file.įLOAT fraction when ranking and computing mapping quality Provided as the target sequences, options Indexing options are fixed in the index file. If even shorter startup time is desired, use this option to save It can index the human genome in a couple When base-level alignment is not requested, this option is automatically applied.įILE.
The index generated with this option will not work with NB: mapping quality is incorrect given aĭont store target sequences in the index. Query.fa multiple times to map it against each batch of target sequences. An HPC sequence is constructed byĬontracting homopolymer runs to a single base. Use homopolymer-compressed (HPC) minimizers. Megabases in length at a error rate ~15%. It works efficiently with query sequences from a few kilobases to ~100 Reference genome optionally with detailed alignment (i.e. Overlaps between long noisy reads, or map long reads or their assemblies to a Minimap2 is a fast sequence mapping and alignment program that can find * Indexing the target sequences (optional): Minimap2 - mapping and alignment between collections of DNA sequences
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