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: 4403
Venue: SIGMOD
Year: 2011
Pagerank: 0.00010004608
Overall Rank: 1,944 | 86.48%
DOI: -

Incoming Non-self Citations Over Time

Authors

Incoming Citations (Sorted by Pagerank)

Showing 9 of 9 citing papers.

Rank	Citing Paper	Year	Venue	Pagerank
2,870	Streaming Similarity Search over one Billion Tweets using Parallel Locality-Sensitive Hashing	2013	VLDB	7.9799783e-05
3,058	Rethinking Data-Intensive Science Using Scalable Analytics Systems	2015	SIGMOD	7.6410159e-05
6,983	A Generic Framework for Efficient and Effective Subsequence Retrieval	2012	VLDB	4.8732757e-05
7,902	Building Highly-Optimized, Low-Latency Pipelines for Genomic Data Analysis	2015	CIDR	4.6215911e-05
9,932	Local Filtering: Improving the Performance of Approximate Queries on String Collections	2015	SIGMOD	4.2500258e-05
11,790	Massively Parallel Processing of Whole Genome Sequence Data: An In-Depth Performance Study	2017	SIGMOD	4.1945683e-05
11,894	Building Highly-Optimized, Low-Latency Pipelines for Genomic Data Analysis	2015	CIDR	4.1945683e-05
12,086	RCSI: Scalable similarity search in thousand(s) of genomes	2013	VLDB	4.1945683e-05
12,139	Massive Genomic Data Processing and Deep Analysis	2012	VLDB	4.1945683e-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
238	Cache Conscious Indexing for Decision-Support in Main Memory	1999	VLDB	0.00031642425
266	Efficient Exact Set-Similarity Joins	2006	VLDB	0.00029718727
1,202	VGRAM: Improving Performance of Approximate Queries on String Collections Using Variable-Length Grams	2007	VLDB	0.00013326298
2,193	Cost-Based Variable-Length-Gram Selection for String Collections to Support Approximate Queries Efficiently	2008	SIGMOD	9.3178557e-05
2,213	n-Gram/2L: A Space and Time Efficient Two-Level n-Gram Inverted Index Structure	2005	VLDB	9.2765152e-05
5,397	Fast nGram-Based String Search Over Data Encoded Using Algebraic Signatures	2007	VLDB	5.5299002e-05
5,812	Reference-Based Alignment in Large Sequence Databases	2009	VLDB	5.3172025e-05

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11,790	Massively Parallel Processing of Whole Genome Sequence Data: An In-Depth Performance Study	2017	SIGMOD	4.1945683e-05
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