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Mapped assembly by bwa aln

This function runs the bwa program using the "aln" method for aligning sequences. It is appropriate for matching most types of short-read data.

The GUI is little more than a wrapper around command line tools, which can essentially be repeatedly manually as follows.

  1. Calculate and save the consensus for all contigs in the database in fastq format.
  2. Index the consensus sequence using "bwa index".
  3. Map our input data against the bwa index using "bwa aln". Repeat for reverse matches too.
  4. Generate SAM format from the alignments using "bwa samse" or "bwa sampe".
  5. Convert to BAM and sort by position.
  6. Import the BAM file, appending to the existing gap5 database (equivalent to tg_index -a).

Mapped assembly by bwa dbwtsw

This function runs the bwa program using the "dbwtsw" method for aligning sequences. This should be used when attempting to align longer sequences or data with lots of indels.

The GUI is little more than a wrapper around command line tools, which can essentially be repeatedly manually as follows.

  1. Calculate and save the consensus for all contigs in the database in fastq format.
  2. Index the consensus sequence using "bwa index".
  3. Map our input data against the bwa index using "bwa dbwtsw".
  4. Convert to BAM and sort by position.
  5. Import the BAM file, appending to the existing gap5 database (equivalent to tg_index -a).

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Last generated on 25 November 2011.