| Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks | 2003/11/01 | English | 28,590 |
| The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data | 2010/07/19 | English | 16,739 |
| WebLogo: A Sequence Logo Generator: Figure 1 | 2004/06/01 | English | 8,648 |
| Circos: An information aesthetic for comparative genomics | 2009/06/18 | English | 7,093 |
| Velvet: Algorithms for de novo short read assembly using de Bruijn graphs | 2008/03/18 | English | 7,019 |
| Most mammalian mRNAs are conserved targets of microRNAs | 2008/10/27 | English | 5,840 |
| CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes | 2015/05/14 | English | 5,772 |
| The Human Genome Browser at UCSC | 2002/05/16 | English | 5,198 |
| Fast model-based estimation of ancestry in unrelated individuals | 2009/07/31 | English | 4,998 |
| Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy Assessment | 1998/03/01 | English | 4,689 |
| OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes | 2003/09/01 | English | 4,173 |
| Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation | 2017/03/15 | English | 4,144 |
| Real time quantitative PCR. | 1996/10/01 | English | 3,867 |
| CAP3: A DNA Sequence Assembly Program | 1999/09/01 | English | 3,699 |
| The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression | 2012/09/01 | English | 3,537 |
| Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements | 2004/07/01 | English | 3,231 |
| Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities | 1998/03/01 | English | 3,219 |
| VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing | 2012/02/02 | English | 3,205 |
| GENCODE: The reference human genome annotation for The ENCODE Project | 2012/09/01 | English | 3,080 |
| BLAT—The BLAST-Like Alignment Tool | 2002/03/20 | English | 2,786 |
| Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes | 2005/07/15 | English | 2,586 |
| Consed: A Graphical Tool for Sequence Finishing | 1998/03/01 | English | 2,571 |
| Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons | 2011/01/06 | English | 2,553 |
| ABySS: A parallel assembler for short read sequence data | 2009/02/27 | English | 2,395 |
| The Significance of Digital Gene Expression Profiles | 1997/10/01 | English | 2,226 |
| Maftools: efficient and comprehensive analysis of somatic variants in cancer | 2018/10/19 | English | 2,191 |
| PANTHER: A Library of Protein Families and Subfamilies Indexed by Function | 2003/09/01 | English | 2,157 |
| De novo assembly of human genomes with massively parallel short read sequencing | 2009/12/17 | English | 2,101 |
| MEGAN analysis of metagenomic data | 2007/01/25 | English | 2,058 |
| metaSPAdes: a new versatile metagenomic assembler | 2017/03/15 | English | 1,993 |