Running bowtie:

• Build the index
  • bowtie-build ref.fasta reference
• Single-end alignments
  • bowtie -S reference reads.fastq output.sam (-S required for SAM output)

Running bwa

• Build the index
  • bwa index ref.fasta
• Single-end alignment
  • bwa aln ref.fasta reads.fastq > output.sai
• Convert to SAM
  • bwa samse ref.fasta output.sai reads.fastq > output.sam

Running Mosaik

• Build the index
  • MosaikBuild -fr ref.fasta -oa ref.dat
• Convert the reads
  • MosaikBuild -q reads.fastq -out reads.dat -st illumina (illumina is the machine the reads were produced by)
• Single-end alignments
  • MosaikAligner -in reads.dat -out output.dat -ia ref.dat -hs 14 -act 17 -mm 2 unique
• Convert to SAM
  • MosaikText -in output.dat -sam output.sam

Note that the above was adapted from the Build and Align scripts from in the data directory of the Mosaik download.

If all went well, you should obtain an output.sam file, using any of the above programs...

You can then display this using SAMTools:

• Index the reference
  • samtools faidx ref.fasta
• Convert SAM to BAM
  • samtools import ref.fasta output.sam output.bam
• Sort the BAM (orders the reads by positions in the reference)
  • samtools sort output.bam sorted (will create sorted.bam)
• Index the sorted BAM (unsorted BAM files cannot be indexed)
  • samtools index sorted.bam
• Display
  • samtools tview sorted.bam ref.fasta

On a side note, you can convert a BAM file to a SAM file like so:

• samtools view sorted.bam > sorted.sam

As typing these can be a real pain, I actually automate the process using batch files...