WHAM: A High-throughput Sequence Alignment Method

Summary: WHAM: high-throughput short-read alignment using hash-based indexing and bitwise ops, enabling richer match models than prior aligners. Significant speedups over state-of-the-art; code at http://www.cs.wisc.edu/wham/. (summarized by gpt-5-nano on Feb 09 2026)

Paper ID: 4465
Venue: SIGMOD
Year: 2011
Pagerank: 8.550768e-05
Overall Rank: 2,459 | 83.14%
DOI: 10.1145/1989323.1989370

Incoming Non-self Citations Over Time

Authors

1. Yinan Li (University of Wisconsin)
2. Allison Terrell (University of Wisconsin)
3. Jignesh M. Patel (University of Wisconsin)

BibTeX Citation

@inproceedings{li_sigmod11,
        title = {{WHAM: A High-throughput Sequence Alignment Method}},
        author = {Li, Yinan and Terrell, Allison and Patel, Jignesh M.},
        series = {{SIGMOD} '11},
        booktitle = {Proceedings of the {ACM} {SIGMOD} International Conference on Management of Data},
        publisher = {Association for Computing Machinery},
        doi = {10.1145/1989323.1989370},
        url = {https://dl.acm.org/doi/10.1145/1989323.1989370},
        year = {2011}
}

Incoming Citations (Sorted by Pagerank)

Showing 8 of 8 citing papers.

Rank	Citing Paper	Year	Venue	Pagerank
2,390	Streaming Similarity Search over one Billion Tweets using Parallel Locality-Sensitive Hashing	2013	VLDB	8.6438351e-05
3,552	Rethinking Data-Intensive Science Using Scalable Analytics Systems	2015	SIGMOD	7.3188008e-05
6,858	A Generic Framework for Efficient and Effective Subsequence Retrieval	2012	VLDB	5.7523396e-05
8,429	Building Highly-Optimized, Low-Latency Pipelines for Genomic Data Analysis	2015	CIDR	5.4263087e-05
10,085	Local Filtering: Improving the Performance of Approximate Queries on String Collections	2015	SIGMOD	5.1559617e-05
11,994	Massively Parallel Processing of Whole Genome Sequence Data: An In-Depth Performance Study	2017	SIGMOD	5.093636e-05
12,283	RCSI: Scalable similarity search in thousand(s) of genomes	2013	VLDB	5.093636e-05
12,335	Massive Genomic Data Processing and Deep Analysis	2012	VLDB	5.093636e-05

Outgoing Citations (Sorted by Pagerank)

Showing 7 of 7 cited papers.

Citations counted here include only citations to other VLDB/SIGMOD/CIDR/PODS papers in this database.

Rank	Cited Paper	Year	Venue	Pagerank
169	Efficient Exact Set-Similarity Joins	2006	VLDB	0.0002743469
204	Cache Conscious Indexing for Decision-Support in Main Memory	1999	VLDB	0.00025342994
1,040	VGRAM: Improving Performance of Approximate Queries on String Collections Using Variable-Length Grams	2007	VLDB	0.00012466499
2,103	Cost-Based Variable-Length-Gram Selection for String Collections to Support Approximate Queries Efficiently	2008	SIGMOD	9.1621686e-05
2,262	n-Gram/2L: A Space and Time Efficient Two-Level n-Gram Inverted Index Structure	2005	VLDB	8.8440146e-05
5,691	Fast nGram-Based String Search Over Data Encoded Using Algebraic Signatures	2007	VLDB	6.120274e-05
6,182	Reference-Based Alignment in Large Sequence Databases	2009	VLDB	5.9493566e-05

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2	11,994	Massively Parallel Processing of Whole Genome Sequence Data: An In-Depth Performance Study	2017	SIGMOD
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