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Blasr Installation Qs and As

Blasr Output Formats

Blasr Advanced Options:

• To produce alignments in favor of substitutions instead of short indels

• [To align very short reads using blasr] (https://github.com/PacificBiosciences/blasr/wiki/Advanced-options:-to-align-very-short-reads)

• [To align short and nearly identical query and target] (https://github.com/PacificBiosciences/blasr/wiki/To-align-nearly-identical-or-short-query-&-target)

• [To output unaligned PacBio reads in FASTA and FASTQ] (https://github.com/PacificBiosciences/blasr/wiki/To-output-unaligned-PacBio-reads-in-FASTA-and-FASTQ)

• [To align very long & almost identical sequences] (https://github.com/PacificBiosciences/blasr/wiki/To-align-long-and-almost-identical-sequences)

• [To produce SAM output using SAM 1.4 format] (https://github.com/PacificBiosciences/blasr/wiki/To-produce-SAM-output-in-SAM-1.4-format-(specifically,-to-represent-sequence-mismatches-and-matches-with-'X'-and-'='-instead-of-'M'-in-CIGAR)-using--cigarUseSeqMatch)

• [To fileter alignments based on alignment length, accuracy, hit policy and etc.] (https://github.com/PacificBiosciences/blasr/wiki/To-filter-alignments-based-on-alignment-length,-percentage-accuracy,-hit-policy)