[maq-announce] bug in bwa-0.4.1 and the bug fix

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Hello,

Aaron Quinlan has just found a critical bug in bwa's indexer: it  
segfaults if there are no comment texts in the FASTA header line. I  
have fixed the bug and put a new version on the sourceforge. Nothing  
else was changed. Sorry for this obvious bug.

As a compensate, I am forwarding an email originally sent to the  
1000Genomes Project mailing list. It evaluates how different insert  
sizes and read lengths may affect the fraction of genome that is  
sequence-able with short PE reads. This is done by bwa.

Best wishes,

Heng

Begin forwarded message:

> I have simulated read pairs of different lengths/insert sizes and  
> mapped them back to the human genome to see the effect of these  
> factors on the accessibility of the human genome. The basic message  
> is that in comparison to having longer insert size, having longer  
> read length help to access higher fraction of the human genome with  
> short reads. For example, given 50bp reads, 200+/-20 insert size  
> (50@200+/-20), about 95% of genomes can be covered by uniquely  
> mapped read pairs. This percentage increases to 96% given  
> 50@10000+/-100 PE reads. In contrast, 32@500+/-50 PE reads can  
> access 91% of the genome, while 125@500+/-50 access nearly 98%.
>
> Detailed numbers are attached. Each data line shows mapping quality  
> interval (06x stands for 60-69), # wrong alignments, # alignments in  
> the interval, cumulative # alignments, cumulative alignment error  
> rate.
>
> regards,
>
> Heng
>
> Procedure
> ---------
>
> In simulation, I first simulated a diploid genome with 0.09% SNP  
> rates and 0.01% indel rates. About 1,854,000 PE reads (not 2 million  
> because the simulator may generates a read full of N) were randomly  
> generated from this diploid genome with a uniform 1.5% base error  
> rate. These reads were then mapped back to the human reference  
> genome with bwa. As the simulator coded the true alignment  
> coordinates in the read names, the alignment error rate can be  
> evaluated. Bwa aligner achieves similar accuracy to maq <http://maq.sourceforge.net/bwa-man.shtml#9 
> >. Doing the evaluation with maq would lead to a similar conclusion.  
> Using other aligners may be different.
>
> Results
> -------
>
> ::::::::::::::
> 50bp PE reads; 200+/-20bp insert size
> ::::::::::::::
> 06x            6 / 1535520            1535520  3.907e-06
> 05x            0 / 1188               1536708  3.904e-06
> 04x            2 / 15234              1551942  5.155e-06
> 03x          227 / 115113             1667055  1.410e-04
> 02x         1816 / 81863              1748918  1.173e-03
> 01x           38 / 4518               1753436  1.191e-03
> 00x        60137 / 98102              1851538  3.361e-02
> ::::::::::::::
> 50bp PE reads; 500+/-50bp insert size
> ::::::::::::::
> 06x            4 / 1528486            1528486  2.617e-06
> 05x            0 / 1128               1529614  2.615e-06
> 04x            0 / 12958              1542572  2.593e-06
> 03x          334 / 131015             1673587  2.020e-04
> 02x         1723 / 83586              1757173  1.173e-03
> 01x           44 / 4156               1761329  1.195e-03
> 00x        56826 / 90559              1851888  3.182e-02
> ::::::::::::::
> 50bp PE reads; 3000+/-300bp insert size
> ::::::::::::::
> 06x           12 / 1513600            1513600  7.928e-06
> 05x            0 / 1162               1514762  7.922e-06
> 04x            3 / 10622              1525384  9.834e-06
> 03x          572 / 151097             1676481  3.501e-04
> 02x         1503 / 91113              1767594  1.182e-03
> 01x           33 / 3373               1770967  1.199e-03
> 00x        50185 / 79209              1850176  2.827e-02
> ::::::::::::::
> 50bp PE reads; 10000+/-1000bp insert size
> ::::::::::::::
> 06x           16 / 1505430            1505430  1.063e-05
> 05x            0 / 1140               1506570  1.062e-05
> 04x            1 / 9606               1516176  1.121e-05
> 03x          663 / 163353             1679529  4.049e-04
> 02x         1447 / 95911              1775440  1.198e-03
> 01x           13 / 2700               1778140  1.204e-03
> 00x        45914 / 72701              1850841  2.596e-02
>
>
> ********************************************************
> ********************************************************
>
> ::::::::::::::
> 32bp reads; 500+/-50
> ::::::::::::::
> 06x            8 / 1313464            1313464  6.091e-06
> 05x            0 / 7402               1320866  6.057e-06
> 04x            2 / 25204              1346070  7.429e-06
> 03x          399 / 176376             1522446  2.686e-04
> 02x         2726 / 168809             1691255  1.854e-03
> 01x           52 / 4955               1696210  1.879e-03
> 00x        99521 / 155509             1851719  5.547e-02
> ::::::::::::::
> 50bp reads; 500+/-50
> ::::::::::::::
> 06x            4 / 1528486            1528486  2.617e-06
> 05x            0 / 1128               1529614  2.615e-06
> 04x            0 / 12958              1542572  2.593e-06
> 03x          334 / 131015             1673587  2.020e-04
> 02x         1723 / 83586              1757173  1.173e-03
> 01x           44 / 4156               1761329  1.195e-03
> 00x        56826 / 90559              1851888  3.182e-02
> ::::::::::::::
> 70bp reads; 500+/-50
> ::::::::::::::
> 06x            1 / 1637726            1637726  6.106e-07
> 05x            0 / 390                1638116  6.105e-07
> 04x            0 / 7698               1645814  6.076e-07
> 03x          272 / 93750              1739564  1.569e-04
> 02x          985 / 45099              1784663  7.049e-04
> 01x           26 / 3587               1788250  7.180e-04
> 00x        38266 / 64061              1852311  2.135e-02
> ::::::::::::::
> 125bp reads; 500+/-50
> ::::::::::::::
> 06x            4 / 1711262            1711262  2.337e-06
> 05x            0 / 118                1711380  2.337e-06
> 04x            0 / 4390               1715770  2.331e-06
> 03x          109 / 72593              1788363  6.319e-05
> 02x          381 / 21586              1809949  2.729e-04
> 01x           29 / 2950               1812899  2.885e-04
> 00x        22920 / 40478              1853377  1.265e-02

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