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REDHORSE Package
Example Data | | Generating the input data | | The sequencers such as from Illumina
generate millions of short sequence segments called reads. Each base in
a read has quality associated with it. The output from the sequencers
is therefore in fastq format which includes both the reads as well as
their quality information. The foremost step in the analysis is to
align these reads to the reference genome to find the order of
arrangement of these reads. A variety of aligners such as BOWTIE, BWA, NOVOALIGN and CLC bio exist for this task. One of the outputs of these alignment algorithms is sequence alignment map (SAM) format. The SAM file can be converted into a binary alignment map (BAM) format and sorted using tools such as samtools. This sorted BAM file is the input to REDHORSE. | Index of Utilities
Analytical Pipeline |
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