The latest BWA-SW also works for paired-end reads longer than 100bp. In comparison to BWA-short, BWA-SW tends to be more accurate for highly unique reads and more robust to relative long INDELs and structural variants. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. The Williams and Wilkins Co., Baltimore, Md. References ^ Bergey’s Manual of Systematic Bacteriology Book Review Int. J. of Syst. Collect from the recipient any recipient responsible overpayments. A county responsible overpayment is collected by State Office adjustment. If a family unit is ineligible for a payment from which a collection was deducted, do not credit the family with the deduction. Also, if an overpayment and/or underpayment occur during the same period and are not both recipient responsible, the county cannot determine a net overpayment or underpayment. In these situations, reimburse the recipient for any county responsible underpayments. Indexing smaller genomes with IS algorithms is faster, but requires more memory.
Longer gaps may be found if maxGapE is positive, but it is not guaranteed to find all hits. When performing SW extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best SW score minus the clipping penalty, clipping will not be applied. This option may dramatically reduce the redundancy of output when mapping long contig or BAC sequences. -M Mark shorter split hits as secondary (for Picard compatibility). -v INT Control the verbose level of the output. The BWA-MEM algorithm performs local alignment. It may produce multiple primary alignments for different part of a query sequence. Bioinformatics, 28, 1838-1844. [PMID: 22569178] The BWA-MEM algorithm has not been published yet. HISTORY BWA is largely influenced by BWT-SW. It uses source codes from BWT-SW and mimics its binary file formats; BWA-SW resembles BWT-SW in several ways.
The speed of alignment is largely determined by the error rate of the query sequences (r). Firstly, BWA runs much faster for near perfect hits than for hits with many differences, and it stops searching for a hit with l+2 differences if a l-difference hit is found. One may consider to use option -M to flag shorter split hits as secondary. OPTIONS: -t INT Number of threads  -k INT Minimum seed length. Baltimore. Bergey’s Manual of Systematic Bacteriology, 1st ed. Krieg, N.R. & Holt, J.C. (eds., 1984). Bergey’s Manual of Systematic Bacteriology, 1st ed., vol. 1, Williams and Wilkins, Baltimore. Staley, J.T., Bryant, M.P., Pfennig, N. & Holt, J.G. (eds., 1989). Bergey’s Manual of Systematic Bacteriology, 1st ed., vol. 3, Williams and Wilkins, Baltimore. Bergey’s Manual of Systematic Bacteriology. 4 (2nd ed.). New York: Springer. p. 1750. ISBN 978-0-387-95043-3. British Library no. GBA561951. ^ «Bergey’s Manual of Systematic Bacteriology», Book Reviews, Notes, and Listings, Annals of Internal Medicine External links. When seeding is enabled, BWA further requires that the first seedLen subsequence contains no more than maxSeedDiff differences.