Milestones in computational methods
The milestones listed below correspond to key developments in the new computational tools and bioinformatics methods for processing and analyses of sequencing data. This is a large area and we apologize for any omissions.
1981: Smith–Waterman
1982: GenBank/ENA/DDBJ
1990: BLAST
1995: TIGR assembler
1996: RepeatMasker
1997: GENSCAN
1998: phred, phrap, consed: phred introduced quantitative, reliable metrics for base quality, substituting human judgement with computers, a process that occurred repeatedly over the course of the Human Genome Project.
2000: Celera assembler
2001: Bioconductor
2001: EULER
2002: BLAT
2002: UCSC Genome Browser
2002: Ensembl
2005: Galaxy
2007: Short Read Archive (SRA) / European Nucleotide Archive (ENA) / DDBJ
2008: ALLPATHS
2008: Velvet
2009: Bowtie
2009: BWA
2009: SAMtools
2009: BreakDancer
2009: Pindel
2009: TopHat
2010: SOAPdenovo
2010: GATK
2010: Cufflinks
2011: Integrated Genomics Viewer
2013: HGAP/Quiver
2017: Canu