Mercurial > repos > iuc > minimap2
diff minimap2.xml @ 0:2445d53549ba draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
| author | iuc |
|---|---|
| date | Sat, 04 Nov 2017 05:41:11 -0400 |
| parents | |
| children | b103bc946f57 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minimap2.xml Sat Nov 04 05:41:11 2017 -0400 @@ -0,0 +1,539 @@ +<?xml version="1.0"?> +<tool id="minimap2" name="Map with minimap2" version="2.3" profile="17.01"> + <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description> + <requirements> + <requirement type="package" version="2.3">minimap2</requirement> + <requirement type="package" version="1.6">samtools</requirement> + </requirements> + <version_command>minimap2 --version</version_command> + <command> +<![CDATA[ + #if $reference_source.reference_source_selector == 'history': + ln -f -s '$reference_source.ref_file' reference.fa && + #else: + ln -f -s '$reference_source.ref_file.fields.path' reference.fa && + #end if + minimap2 -a + -x $analysis_type_selector + ## indexing options + #if $indexing_options.k: + -k $indexing_options.k + #end if + #if $indexing_options.w: + -w $indexing_options.w + #end if + #if $indexing_options.I: + -I $indexing_options.I + #end if + ## Mapping options + #if $mapping_options.f: + -f $mapping_options.f + #end if + #if $mapping_options.g: + -g $mapping_options.g + #end if + #if $mapping_options.G: + -G $mapping_options.G + #end if + #if $mapping_options.F: + -F $mapping_options.F + #end if + #if $mapping_options.r: + -r $mapping_options.r + #end if + #if $mapping_options.n: + -n $mapping_options.n + #end if + #if $mapping_options.m: + -m $mapping_options.m + #end if + $mapping_options.X + #if $mapping_options.p: + -p $mapping_options.p + #end if + #if $mapping_options.N: + -N $mapping_options.N + #end if + ## Alignment options + #if $alignment_options.A: + -A $alignment_options.A + #end if + #if $alignment_options.B: + -B $alignment_options.B + #end if + #if $alignment_options.O: + #if $alignment_options.O2: + -O $alignment_options.O,$alignment_options.O2 + #end if + -O $alignment_options.O + #end if + #if $alignment_options.E: + #if $alignment_options.E2: + -E $alignment_options.E,$alignment_options.E2 + #else + -E $alignment_options + #end if + #end if + #if $alignment_options.z: + $alignment_options.z + #end if + #if $alignment_options.s: + -s $alignment_options.s + #end if + #if $alignment_options.u: + -u $alignment_options.u + #end if + ## Output options + $io_options.Q + $io_options.L + #if $io_options.cs: + --cs $io_options.cs + #end if + #if $io_options.K: + -K $io_options.K + #end if + -t \${GALAXY_SLOTS:-4} + reference.fa + #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']: + '$fastq_input.fastq_input1' + #else if $fastq_input.fastq_input_selector == 'paired': + '$fastq_input.fastq_input1' '$fastq_input.fastq_input2' + #else if $fastq_input.fastq_input_selector == 'paired_collection': + '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse' + #end if + | samtools sort + -@\${GALAXY_SLOTS:-2} + -O $io_options.output_format + #if $io_options.output_format == 'CRAM': + --reference reference.fa + #end if + -o '$alignment_output' +]]> + </command> + <inputs> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> + <option value="cached">Use a built-in genome index</option> + <option value="history">Use a genome from history and build index</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No reference genomes are available" /> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + <section name="indexing_options" title="Indexing options"> + <!-- Homopolymer setting seems to not properly overwrite sr preset + <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/> + --> + <param argument="-k" type="integer" min="4" max="28" optional="true" label="k-mer size" help=""/> + <param argument="-w" type="integer" min="1" optional="true" label="minimizer window size" help=""/> + <param argument="-I" type="integer" min="1" optional="true" label="split index for every N input gigabases" help=""/> + </section> + <!-- start unchanged copy from bwa-mem --> + <conditional name="fastq_input"> + <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> + <option value="single">Single</option> + <option value="paired">Paired</option> + <option value="paired_collection">Paired Collection</option> + <option value="paired_iv">Paired Interleaved</option> + </param> + <when value="paired"> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/> + </when> + <when value="single"> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> + </when> + <when value="paired_collection"> + <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> + </when> + <when value="paired_iv"> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> + </when> + </conditional> + <!-- end unchanged copy from bwa-mem --> + <param name="analysis_type_selector" type="select" label="Select analysis mode (sets default)"> + <option value="map-pb">-Hk19 (PacBio vs reference mapping)</option> + <option value="map-ont">-k15 (Oxford Nanopore vs reference mapping)</option> + <option value="asm5">-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5% div.)</option> + <option value="asm10">-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10% div.)</option> + <option value="ava-pb">-Hk19 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25 (PacBio read overlap)</option> + <option value="ava-ont">-k15 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25 (ONT read overlap)</option> + <option value="splice">long-read spliced alignment</option> + <option value="sr">short single-end reads without splicing</option> + </param> + <section name="mapping_options" title="Set advanced mapping options" help="Sets -f, -g, -G, -F, -r, -n, -m, -X, -p and -N options." expanded="False"> + <param argument="-f" type="float" value="" optional="true" label="filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/> + <param argument="-g" type="integer" value="" optional="true" label="stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/> + <param argument="-G" type="integer" value="" optional="true" label="max intron length in thousand (effective with -xsplice; changing -r)" help="default=200"/> + <param argument="-F" type="integer" value="" optional="true" label="max fragment length (effective with -xsr or in the fragment mode)" help="default=800" /> + <param argument="-r" type="integer" value="" optional="true" label="bandwidth used in chaining and DP-based alignment" help="default=500" /> + <param argument="-n" type="integer" value="" optional="true" label="minimal number of minimizers on a chain" help="default=3"/> + <param argument="-m" type="integer" value="" optional="true" label="minimal chaining score (matching bases minus log gap penalty)" help="default=40"/> + <param argument="-X" type="boolean" truevalue="-X" falsevalue="" optional="true" label="skip self and dual mappings (for the all-vs-all mode)"/> + <param argument="-p" type="float" value="" max="1" optional="true" label="min secondary-to-primary score ratio" help="default=0.8"/> + <param argument="-N" type="integer" min="0" optional="true" label="retain at most INT secondary alignments" help="default=5"/> + </section> + <section name="alignment_options" title="Set advanced alignment options" help="Sets -A, -B, -O, -E, -z, -s and -u options." expanded="False"> + <param argument="-A" type="integer" optional="true" label="Score for a sequence match" help="default=2"/> + <param argument="-B" type="integer" optional="true" label="Penalty for a mismatch" help="-B; default=4" /> + <param argument="-O" type="integer" min="0" optional="true" label="Gap open penalties for deletions" help="-O; default=4"/> + <param name="-O2" type="integer" min="0" optional="true" label="Gap open penalties for insertions" help="-O; default=24"/> + <param argument="-E" type="integer" min="0" optional="true" label="Gap extension penalties; a gap of size k cost '-O + -E*k'. If two numbers are specified, the first is the penalty of extending a deletion and the second for extending an insertion" help="-E; default=2"/> + <param name="E2" type="integer" min="0" optional="true" label="Gap extension penalty for extending an insertion; if left empty uses the value specified for Gap extension penalties above" help="-E; default=1"/> + <param argument="-z" type="integer" optional="true" label="Z-drop score" help="default=400"/> + <param argument="-s" type="integer" optional="true" label="minimal peak DP alignment score" help="default=80"/> + <param argument="-u" type="select" optional="true" label="how to find GT-AG"> + <option value="n">don't match GT-AG</option> + <option value="f">transcript strand</option> + <option value="b">both strands</option> + </param> + </section> + <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False"> + <param name="output_format" type="select" label="Produce BAM or CRAM file?"> + <option value="BAM">BAM</option> + <option value="CRAM">CRAM</option> + </param> + <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" optional="true" label="don't output base quality"/> + <param argument="-L" type="boolean" truevalue="-L" falsevalue="" optional="true" label="write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/> + <param argument="-K" type="integer" optional="true" label="minibatch size for mapping (in megabyte)" help="default=500M"/> + <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below."> + <option value="none">no</option> + <option value="short">short</option> + <option value="long">long</option> + </param> + </section> + </inputs> + <outputs> + <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)"> + <actions> + <conditional name="reference_source.reference_source_selector"> + <when value="cached"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="all_fasta" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="reference_source.ref_file" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + <change_format> + <when input="io_options.output_format" value="CRAM" format="cram" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <!-- test single input --> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + <param name="fastq_input_selector" value="single"/> + <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> + <param name="analysis_type_selector" value="sr"/> + <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" /> + </test> + <test> + <!-- test cram output --> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + <param name="fastq_input_selector" value="single"/> + <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> + <param name="analysis_type_selector" value="sr"/> + <param name="output_format" value="CRAM"/> + <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" /> + </test> + <test> + <!-- test paired input --> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> + <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> + <param name="analysis_type_selector" value="sr"/> + <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" /> + </test> + <test> + <!-- test paired input with one pair compressed --> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> + <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> + <param name="analysis_type_selector" value="sr"/> + <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" /> + </test> + <test> + <!-- test collection input --> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + <param name="fastq_input_selector" value="paired_collection"/> + <param name="fastq_input1"> + <collection type="paired"> + <element name="forward" value="bwa-mem-fastq1.fq" /> + <element name="reverse" value="bwa-mem-fastq2.fq" /> + </collection> + </param> + <param name="analysis_type_selector" value="sr"/> + <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="2" /> + </test> + <test> + <!-- test data table reference --> + <param name="reference_source_selector" value="cached" /> + <param name="ref_file" value="bwa-mem-mt-genome"/> + <param name="fastq_input_selector" value="single"/> + <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> + <param name="analysis_type_selector" value="sr"/> + <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" /> + </test> + </tests> + <help> + +Users’ Guide +------------ + +Minimap2 is a versatile sequence alignment program that aligns DNA or +mRNA sequences against a large reference database. Typical use cases +include: (1) mapping PacBio or Oxford Nanopore genomic reads to the +human genome; (2) finding overlaps between long reads with error rate up +to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA +or Direct RNA reads against a reference genome; (4) aligning Illumina +single- or paired-end reads; (5) assembly-to-assembly alignment; (6) +full-genome alignment between two closely related species with +divergence below ~15%. + +For ~10kb noisy reads sequences, minimap2 is tens of times faster than +mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It +is more accurate on simulated long reads and produces biologically +meaningful alignment ready for downstream analyses. For >100bp Illumina +short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and +as accurate on simulated data. Detailed evaluations are available from +the `minimap2 preprint`. + +General usage +~~~~~~~~~~~~~ + +Minimap2 seamlessly works with gzip’d FASTA and FASTQ formats as input. +You don’t need to convert between FASTA and FASTQ or decompress gzip’d +files first. + +For the human reference genome, minimap2 takes a few minutes to generate +a minimizer index for the reference before mapping. To reduce indexing +time, you can optionally save the index with option **-d** and replace +the reference sequence file with the index file on the minimap2 command +line: + +***Importantly***, it should be noted that once you build the index, +indexing parameters such as **-k**, **-w**, **-H** and **-I** can’t be +changed during mapping. If you are running minimap2 for different data +types, you will probably need to keep multiple indexes generated with +different parameters. This makes minimap2 different from BWA which +always uses the same index regardless of query data types. + +Use cases +~~~~~~~~~ + +Minimap2 uses the same base algorithm for all applications. However, due +to the different data types it supports (e.g. short vs long reads; DNA +vs mRNA reads), minimap2 needs to be tuned for optimal performance and +accuracy. It is usually recommended to choose a preset with option +**-x**, which sets multiple parameters at the same time. The default +setting is the same as ``map-ont``. + +Map long noisy genomic reads +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The difference between ``map-pb`` and ``map-ont`` is that ``map-pb`` +uses homopolymer-compressed (HPC) minimizers as seeds, while ``map-ont`` +uses ordinary minimizers as seeds. Emperical evaluation suggests HPC +minimizers improve performance and sensitivity when aligning PacBio +reads, but hurt when aligning Nanopore reads. + +Map long mRNA/cDNA reads +^^^^^^^^^^^^^^^^^^^^^^^^ + + +There are different long-read RNA-seq technologies, including +tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq +and Direct RNA-seq. They produce data of varying quality and properties. +By default, ``-x splice`` assumes the read orientation relative to the +transcript strand is unknown. It tries two rounds of alignment to infer +the orientation and write the strand to the ``ts`` SAM/PAF tag if +possible. For Iso-seq, Direct RNA-seq and tranditional full-length +cDNAs, it would be desired to apply ``-u f`` to force minimap2 to +consider the forward transcript strand only. This speeds up alignment +with slight improvement to accuracy. For noisy Nanopore Direct RNA-seq +reads, it is recommended to use a smaller k-mer size for increased +sensitivity to the first or the last exons. + +It is worth noting that by default ``-x splice`` prefers +GT[A/G]..[C/T]AG over GT[C/T]..[A/G]AG, and then over other splicing +signals. Considering one additional base improves the junction accuracy +for noisy reads, but reduces the accuracy when aligning against the +widely used SIRV control data. This is because SIRV does not honor the +evolutionarily conservative splicing signal. If you are studying SIRV, +you may apply ``--splice-flank=no`` to let minimap2 only model GT..AG, +ignoring the additional base. + +Find overlaps between long reads +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Similarly, ``ava-pb`` uses HPC minimizers while ``ava-ont`` uses +ordinary minimizers. It is usually not recommended to perform base-level +alignment in the overlapping mode because it is slow and may produce +false positive overlaps. However, if performance is not a concern, you +may try to add ``-a`` or ``-c`` anyway. + +Map short accurate genomic reads +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + + +When two read files are specified, minimap2 reads from each file in turn +and merge them into an interleaved stream internally. Two reads are +considered to be paired if they are adjacent in the input stream and +have the same name (with the ``/[0-9]`` suffix trimmed if present). +Single- and paired-end reads can be mixed. + +Minimap2 does not work well with short spliced reads. There are many +capable RNA-seq mappers for short reads. + +Full genome/assembly alignment +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +For cross-species full-genome alignment, the scoring system needs to be +tuned according to the sequence divergence. + +Advanced features +~~~~~~~~~~~~~~~~~ + +Working with >65535 CIGAR operations +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Due to a design flaw, BAM does not work with CIGAR strings with >65535 +operations (SAM and CRAM work). However, for ultra-long nanopore reads +minimap2 may align ~1% of read bases with long CIGARs beyond the +capability of BAM. If you convert such SAM/CRAM to BAM, Picard and +recent samtools will throw an error and abort. Older samtools and other +tools may create corrupted BAM. + +To avoid this issue, you can add option ``-L`` at the minimap2 command +line. This option moves a long CIGAR to the ``CG`` tag and leaves a +fully clipped CIGAR at the SAM CIGAR column. Current tools that don’t +read CIGAR (e.g. merging and sorting) still work with such BAM records; +tools that read CIGAR will effectively ignore these records. I have pull +requests to the SAM spec, htslib, htsjdk, bedtools2, Rsamtools and +igv.js. If they are accepted, future versions of these tools will +seamlessly recognize long-cigar records generated by option ``-L``. + +**TD;DR**: if you work with ultra-long reads and use tools that only +process BAM files, please add option ``-L``. + +The cs optional tag +^^^^^^^^^^^^^^^^^^^ + +The ``cs`` SAM/PAF tag encodes bases at mismatches and INDELs. It +matches regular expression +``/(:[0-9]+|\*[a-z][a-z]|[=\+\-][A-Za-z]+)+/``. Like CIGAR, ``cs`` +consists of series of operations. Each leading character specifies the +operation; the following sequence is the one involved in the operation. + +The ``cs`` tag is enabled by command line option ``--cs``. The following +alignment, for example: + +.. code:: + + CGATCGATAAATAGAGTAG---GAATAGCA + |||||| |||||||||| |||| ||| + CGATCG---AATAGAGTAGGTCGAATtGCA + +is represented as ``:6-ata:10+gtc:4*at:3``, where ``:[0-9]+`` represents +an identical block, ``-ata`` represents a deltion, ``+gtc`` an insertion +and ``*at`` indicates reference base ``a`` is substituted with a query +base ``t``. It is similar to the ``MD`` SAM tag but is standalone and +easier to parse. + +If ``--cs=long`` is used, the ``cs`` string also contains identical +sequences in the alignment. The above example will become +``=CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA``. The long form of ``cs`` +encodes both reference and query sequences in one string. + +Algorithm overview +~~~~~~~~~~~~~~~~~~ + +In the following, minimap2 command line options have a dash ahead and +are highlighted in bold. The description may help to tune minimap2 +parameters. + +1. Read **-I** [=*4G*] reference bases, extract + (**-k**,\ **-w**)-minimizers and index them in a hash table. + +2. Read **-K** [=*200M*] query bases. For each query sequence, do step 3 + through 7: + +3. For each (**-k**,\ **-w**)-minimizer on the query, check against the + reference index. If a reference minimizer is not among the top **-f** + [=*2e-4*] most frequent, collect its the occurrences in the + reference, which are called *seeds*. + +4. Sort seeds by position in the reference. Chain them with dynamic + programming. Each chain represents a potential mapping. For read + overlapping, report all chains and then go to step 8. For reference + mapping, do step 5 through 7: + +5. Let *P* be the set of primary mappings, which is an empty set + initially. For each chain from the best to the worst according to + their chaining scores: if on the query, the chain overlaps with a + chain in *P* by **–mask-level** [=*0.5*] or higher fraction of the + shorter chain, mark the chain as *secondary* to the chain in *P*; + otherwise, add the chain to *P*. + +6. Retain all primary mappings. Also retain up to **-N** [=*5*] top + secondary mappings if their chaining scores are higher than **-p** + [=*0.8*] of their corresponding primary mappings. + +7. If alignment is requested, filter out an internal seed if it + potentially leads to both a long insertion and a long deletion. + Extend from the left-most seed. Perform global alignments between + internal seeds. Split the chain if the accumulative score along the + global alignment drops by **-z** [=*400*], disregarding long gaps. + Extend from the right-most seed. Output chains and their alignments. + +8. If there are more query sequences in the input, go to step 2 until no + more queries are left. + +9. If there are more reference sequences, reopen the query file from the + start and go to step 1; otherwise stop. + +Limitations +----------- + +- Minimap2 may produce suboptimal alignments through long + low-complexity regions where seed positions may be suboptimal. This + should not be a big concern because even the optimal alignment may be + wrong in such regions. + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btp324</citation> + <citation type="doi">10.1093/bioinformatics/btp698</citation> + <citation type="bibtex">@misc{1303.3997, + Author = {Heng Li}, + Title = {Minimap2: fast pairwise alignment for long nucleotide sequences}, + Year = {2017}, + Eprint = {arXiv:1708.01492}, + url = {https://arxiv.org/abs/1708.01492}, + }</citation> + </citations> +</tool>