List of tools provided by my prof
1. bowtie (http://bowtie-bio.sourceforge.net/)
This program maps sequence reads to a reference genome. It is a most recent program. It is very fast. It still does not address indels and paired-end reads.
2. Maq (http://maq.sourceforge.net/)
This program is more mature and address many different needs including mapping reads to a reference genome, constructing consensus sequences, identifying SNPs and indels. It also comes with many useful utility programs such as a reformating program.
3. SOAP (http://soap.genomics.org.cn/)
This program does similar jobs as Maq. It was used for assembling the first Asian genome (http://www.nature.com/nature/journal/v456/n7218/abs/nature07484.html). Some functions are coming.
4. velvet (http://www.ebi.ac.uk/~zerbino/velvet/)
This is a de novo reads assembler. It assembles sequences reads into long contigs without relying on a reference genome. It will be useful for closing some gaps and identifying genomic regions that are not present in the reference sequence.
5 BLAT (http://genome.ucsc.edu/FAQ/FAQblat)
This program is good for aligning highly similar sequences.
6. GBrowse (http://gmod.org/wiki/Gbrowse)
This software is very useful for displaying alignment and for identifying automatically sequence features.
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