Page Index - pb-cdunn/blasr GitHub Wiki

21 page(s) in this GitHub Wiki:

• Home
• Advanced options: to align very short reads
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• Advanced options: to produce alignments in favor of substitutions instead of short indels.
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• Blasr Installation Qs & As
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• Blasr Output Format
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• News
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• To align long and almost identical sequences
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• To align nearly identical or short query & target
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• To filter alignments based on alignment length, percentage accuracy, hit policy
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• To output unaligned PacBio reads in FASTA and FASTQ
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• 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
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