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Welcome to the blasr wiki!
When reporting any issue in blasr, please, always provide the following info
- Did you install via bioconda or SMRT Analysis build? Source builds are not supported!
- OS version : output of "uname -a"
- Blasr version : output of "blasr --version"
- Exact and complete Blasr invocation command and its output
Blasr Advanced Tutorial:
- To place gap consistently for variant caller
- To produce alignments in favor or indels instead of substitutions
- To produce alignments in favor of substitutions instead of short indels
- To align very short reads using blasr
- maxMatch must be properly set to align almost identical reads
- To align short and nearly identical query and target
- To align very long & almost identical sequences
- To align long reads to highly repetitive reference
- To produce SAM output using SAM 1.4 format
- To filter alignments based on alignment length, accuracy, hit policy and etc.
- To output unaligned PacBio reads in FASTA and FASTQ
- HitPolicy and bestn
- MapQV Discussion by Mark Chaisson
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