I read BWA manual. Seems for 454 longer reads, it's recommended to use
BWA -BWASW, which only supports single-end reads.
Then what about 454 paired-end reads？Use bowtie? Also, 454 contain reads with variable length. Then how to deal with those very short reads? （I see some reads are only 10bp..) thx
@SRR000945.10444 E78I8DJ01CQCVG length=108 TGACTTTGTAATTTCCATATTTAAATTCCTTCATCTGATTTTCAGCTTCTCAGGGAAACCACCTAATATCCCTACCAGACAGTCATCTTTCATCTACTGAATAATTCC + AAABAAA====AABAAABBA@@AAAAAAABBBBBBBBB@@@@BBBBBBBBBBBAAAAAAABABBBBAAAAAAA@??AAAAAA???@=<<<@??????@@@@?==9995 @SRR000945.10446 E78I8DJ01A06WQ length=10 AACTCCCAGA + 555=555995 @SRR000945.10447 E78I8DJ01A1GWE length=48 GCTCAAATAGTTATCTTCCCTGAGATGCCTCCCACTAACTCACAATCG + AAAA@@@A???AAAA??===?AAAAAA@@@?????@@@???????===