archive:bioinformatic_tools:bwa
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archive:bioinformatic_tools:bwa [2011/05/13 03:01] svohr created |
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| Their are two options for the algorithm. The default option, ''is'', is relatively fast and works on genomes smaller than 2GB. The other algorithm, ''bwtsw'', is slower and less accurate but works on longer reads and works with larger databases. | Their are two options for the algorithm. The default option, ''is'', is relatively fast and works on genomes smaller than 2GB. The other algorithm, ''bwtsw'', is slower and less accurate but works on longer reads and works with larger databases. | ||
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| Next, the reads are aligned to the reference using the ''aln'' command. | Next, the reads are aligned to the reference using the ''aln'' command. | ||
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| </code> | </code> | ||
| + | ====== Determining Paired-End Insert Size ====== | ||
| + | BWA was used to estimate the distribution of insert sizes in the Illumina runs for banana slug. The 454 reads were used as the reference and the Illumina reads were mapped onto them. The distribution of the insert lengths can be inferred from the pairs that map onto the same 454 read. This is possible because our insert sizes are smaller than the size of the 454 reads. | ||
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| + | Here is the frequencies of each inferred insert length from the SAM file from the paired end alignments for Illumina run 2. The mean inferred insert size for the barcode 7 reads is 258 bases and 138 bases for the barcode 8 reads. | ||
| + | {{:bioinformatic_tools:run2_insert_size_histogram.png|}} | ||
archive/bioinformatic_tools/bwa.txt · Last modified: 2015/09/04 09:06 by 68.180.228.52
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