### Alignment Timing and Memory Output Example Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Shows example timing and memory consumption metrics logged when using '--log-level INFO'. This information is crucial for performance analysis and resource management. ```text Index Build/Read Time: 22s 327ms Alignment Time: 5s 523ms Sort Merge Time: 344ms 927us BAI Generation Time: 150ms PBI Generation Time: 161ms 120us Run Time: 28s 392ms CPU Time: 39s 653ms Peak RSS: 12.5847 GB ``` -------------------------------- ### pbmm2 Command Line Options Examples Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Demonstrates various command-line options for pbmm2, including enabling on-the-fly sorting, specifying input datasets for unrolled alignment, overriding sample names, splitting output by sample, stripping tags, including unmapped reads, and setting the number of best alignments. ```bash # Example: On-the-fly sorting pbmm2 align --sort input.bam output.bam # Example: Unrolled alignment with subreadset.xml pbmm2 align --zmw reads.subreadset.xml output.bam # Example: Setting sample name pbmm2 align --sample MySample input.bam output.bam # Example: Splitting output by sample pbmm2 align --split-by-sample input.bam output_prefix # Example: Stripping tags pbmm2 align --strip input.bam output.bam # Example: Including unmapped reads pbmm2 align --unmapped input.bam output.bam # Example: Outputting N best alignments pbmm2 align -N 5 input.bam output.bam # Example: Aligning only the median subread per ZMW pbmm2 align --median-filter input.bam output.bam ``` -------------------------------- ### Alignment Statistics Output Example Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Displays example alignment metrics logged when using '--log-level INFO'. These statistics provide insights into the mapping process, including read counts, mapped bases, and sequence identity. ```text Mapped Reads: 1529671 Alignments: 3087717 Mapped Bases: 28020786811 Mean Sequence Identity: 88.4% Max Mapped Read Length : 122989 Mean Mapped Read Length : 35597.9 ``` -------------------------------- ### Progress Output Example Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Illustrates the progress reporting format when using '--log-level DEBUG'. The output includes the number of reads processed, alignments generated, and reads processed per minute. ```text #Reads, #Aln, #RPM: 1462688, 2941000, 37393 #Reads, #Aln, #RPM: 1465877, 2948000, 37379 #Reads, #Aln, #RPM: 1469103, 2955000, 37350 ``` -------------------------------- ### Index reference for PacBio data alignment Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md This command indexes a reference FASTA file or PacBio XML file to create an .mmi index file. Indexing is recommended for repeated use of the same reference with the same preset. Note that certain alignment parameters cannot be overridden when using an index file. ```bash pbmm2 index ref.fasta ref.mmi --preset SUBREAD ``` -------------------------------- ### pbmm2 Alignment Preset Parameters Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Defines the default parameter sets for different alignment modes in pbmm2: SUBREAD, CCS, HIFI, ISOSEQ, and UNROLLED. These presets optimize alignment based on the expected read characteristics. ```text Alignment modes of --preset: - "SUBREAD" -k 19 -w 19 -o 5 -O 56 -e 4 -E 1 -A 2 -B 5 -z 400 -Z 50 -r 2000 -g 5000 - "CCS" or "HIFI" -k 19 -w 19 -u -o 6 -O 26 -e 2 -E 1 -A 1 -B 4 -z 400 -Z 50 -r 2000 -g 5000 - "ISOSEQ" -k 15 -w 5 -u -o 2 -O 32 -e 1 -E 0 -A 1 -B 2 -z 200 -Z 100 -r 200000 -g 2000 -C 5 -G 200000 - "UNROLLED" -k 15 -w 15 -o 2 -O 32 -e 1 -E 0 -A 1 -B 2 -z 200 -Z 100 -r 2000 -g 10000 Default ["CCS"] ``` -------------------------------- ### Align with File of File Names (fofn) Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Aligns reads from multiple FASTQ files specified in a .fofn file to a reference genome. The .fofn file lists each FASTQ file path on a new line. This allows processing large datasets distributed across many files. ```bash echo "m64001_190131_212703.Q20.fastq.gz" > myfiles.fofn echo "m64001_190228_200412.Q20.fastq.gz" >> myfiles.fofn pbmm2 align hg38.fasta myfiles.fofn hg38.myfiles.bam --rg '@RG\tID:myid\tSM:mysample' ``` -------------------------------- ### Align PacBio reads to reference sequences Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md This command aligns PacBio reads (from BAM, XML, FA, or FQ files) to a reference sequence (FASTA, XML, or MMI index). The output is an aligned BAM file, which can be streamed to stdout if the output file is omitted. Options for parallelization, sorting, and read group information are available. ```bash pbmm2 align ref.mmi movie.subreads.bam ref.movie.bam --preset SUBREAD ``` ```bash pbmm2 align ref.fasta movie.subreads.bam ref.movie.bam --preset SUBREAD --sort -j 4 -J 2 ``` ```bash pbmm2 align ref.fasta movie.subreadset.xml ref.movie.alignmentset.xml --preset SUBREAD --sort ``` ```bash pbmm2 align hg38.mmi movie1.subreadset.xml --preset SUBREAD | samtools sort > hg38.movie1.sorted.bam ``` ```bash pbmm2 align ref.fasta movie.Q20.fastq ref.movie.bam --sort --rg '@RG\tID:myid\tSM:mysample' ``` -------------------------------- ### pbmm2 Alignment Parameter Overrides Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Lists common parameters that can be overridden to fine-tune alignment. This includes k-mer size, minimizer window, matching/mismatch penalties, Z-drop scores, and bandwidth for chaining/DP alignment. ```text -k k-mer size (no larger than 28). [-1] -w Minimizer window size. [-1] -u Disable homopolymer-compressed k-mer (compression is active for SUBREAD & UNROLLED presets). -A Matching score. [-1] -B Mismatch penalty. [-1] -z Z-drop score. [-1] -Z Z-drop inversion score. [-1] -r Bandwidth used in chaining and DP-based alignment. [-1] -g Stop chain enlongation if there are no minimizers in N bp. [-1] ``` -------------------------------- ### Align FASTA/Q with Read Group Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Aligns FASTA/Q reads to a reference genome, specifying a read group identifier and sample name using the --rg option. This is useful for distinguishing different sample sources in sequencing experiments. ```bash pbmm2 align hg38.fasta movie.Q20.fastq hg38.movie.bam --rg '@RG\tID:myid\tSM:mysample' ``` -------------------------------- ### Align BAM Files using fofn Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Aligns reads from multiple BAM files, listed in a .fofn file, to a reference genome. This method is suitable for consolidating alignments from various BAM sources into a single output BAM file. ```bash ls *.subreads.bam > mymovies.fofn pbmm2 align hg38.fasta mymovies.fofn hg38.mymovies.bam ``` -------------------------------- ### pbmm2 Implicit Minimap2 Parameters Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md This section details special parameters implicitly used by pbmm2 to achieve alignment behavior similar to blasr. These include soft clipping, long cigars, --eqx cigars, no overlapping query intervals, and disabling secondary alignments. ```shell # Soft clipping -Y # Long cigars for tag CG -L # X/=` cigars instead of `M` --eqx # No overlapping query intervals (repeated matches trimming) # See README.md#what-is-repeated-matches-trimming # No secondary alignments --secondary=no ``` -------------------------------- ### pbmm2 ISOSEQ Specific Parameter Overrides Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Details additional parameters that can be overridden specifically for the ISOSEQ alignment mode in pbmm2. These include maximum intron length and cost for non-canonical splicing. ```text For `ISOSEQ`, you can override additional parameters: -G Max intron length (changes -r). [-1] -C Cost for a non-canonical GT-AG splicing. [-1] --no-splice-flank Do not prefer splice flanks GT-AG. ``` -------------------------------- ### pbmm2 Sequence Identity Filters Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md pbmm2 provides three filters to remove low-quality alignments: min-concordance-perc, min-id-perc, and min-gap-comp-id-perc. All filters are combined with AND logic. ```shell # --min-concordance-perc: Legacy mapped concordance filter (hidden). # Defined as: 100 - 100 * (#Deletions + #Insertions + #Mismatches) / (AlignEndInRead - AlignStartInRead) # Default: deactivated # --min-id-perc: Sequence identity percentage filter (hidden). # Defined as: 100 * #Matches / (#Matches + #Mismatches + #Deletions + #Insertions) # Default: deactivated # --min-gap-comp-id-perc: Gap-compressed sequence identity filter (default). # Defined as: 100 * #Matches / (#Matches + #Mismatches + #DeletionEvents + #InsertionEvents) # Default: 70% ``` -------------------------------- ### pbmm2 Gap Penalty Overrides Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Specifies parameters for overriding piecewise linear gap penalties in pbmm2 alignments. These options allow customization of the costs associated with opening and extending gaps. ```text -o,--gap-open-1 Gap open penalty 1. [-1] -O,--gap-open-2 Gap open penalty 2. [-1] -e,--gap-extend-1 Gap extension penalty 1. [-1] -E,--gap-extend-2 Gap extension penalty 2. [-1] -L,--lj-min-ratio Long join flank ratio. [-1] ``` -------------------------------- ### pbmm2 Gap-Compressed Identity Definition Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Calculates gap-compressed sequence identity percentage, treating insertions and deletions as single events. This is the default filter and is considered the fairest metric for error rate assessment. Can be deactivated by setting to 0. ```mathematica 100 * #Matches / (#Matches + #Mismatches + #DeletionEvents + #InsertionEvents) ``` -------------------------------- ### pbmm2 Sequence Identity Definition (BLAST Identity) Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Calculates sequence identity percentage based on BLAST identity. It's defined as the ratio of matches to the total number of matches, mismatches, deletions, and insertions. Can be deactivated by setting to 0. ```mathematica 100 * #Matches / (#Matches + #Mismatches + #Deletions + #Insertions) ``` -------------------------------- ### pbmm2 Mapped Concordance Definition Source: https://github.com/pacificbiosciences/pbmm2/blob/develop/README.md Calculates mapped concordance percentage to filter alignments. It's defined as 100 minus the percentage of deletions, insertions, and mismatches relative to the aligned read length. Can be deactivated by setting to 0. ```mathematica 100 - 100 * (#Deletions + #Insertions + #Mismatches) / (AlignEndInRead - AlignStartInRead) ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.