| SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing | Journal of Computational Biology | 2012 | 12K |
| Multiwfn: a multifunctional wavefunction analyzer | Journal of Computational Chemistry | 2012 | 11.6K |
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| The ORCA program system | Wiley Interdisciplinary Reviews: Computational Molecular Science | 2012 | 6.7K |
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| SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes | Bioinformatics | 2012 | 2K |
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| IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth | Bioinformatics | 2012 | 1.8K |
| MissForest--non-parametric missing value imputation for mixed-type data | Bioinformatics | 2012 | 1.6K |
| Unipro UGENE: a unified bioinformatics toolkit | Bioinformatics | 2012 | 1.2K |
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| RSeQC: quality control of RNA-seq experiments | Bioinformatics | 2012 | 1.2K |
| GAPIT: genome association and prediction integrated tool | Bioinformatics | 2012 | 1.1K |
| Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels | Bioinformatics | 2012 | 1.1K |
| Snakemake--a scalable bioinformatics workflow engine | Bioinformatics | 2012 | 1.1K |
| A high-performance computing toolset for relatedness and principal component analysis of SNP data | Bioinformatics | 2012 | 1.1K |
| DELLY: structural variant discovery by integrated paired-end and split-read analysis | Bioinformatics | 2012 | 1.1K |
| New development in freefem++ | Journal of Numerical Mathematics | 2012 | 1K |
| Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs | Bioinformatics | 2012 | 1K |
| Matrix eQTL: ultra fast eQTL analysis via large matrix operations | Bioinformatics | 2012 | 896 |
| Natural bond orbital methods | Wiley Interdisciplinary Reviews: Computational Molecular Science | 2012 | 887 |
| Automated Solution of Differential Equations by the Finite Element Method | Lecture Notes in Computational Science and Engineering | 2012 | 875 |
| ART: a next-generation sequencing read simulator | Bioinformatics | 2012 | 800 |
