Dear seqanswers community,
The alignment step is very long to my mind. I would know how to reduce this time (24h to align one fastq file). Currently, I use the BWA-Backtrack algorithm to align my files.
My fastq files have these characteristics :
Size : About 2 Go
Encoding : Sanger / Illumina 1.9
Total Sequences : about 13 000 000
Sequence length : 51
What can I do to reduce alignment time ? Maybe I should use an other algorithm.
Thanks in advance for your help.
The alignment step is very long to my mind. I would know how to reduce this time (24h to align one fastq file). Currently, I use the BWA-Backtrack algorithm to align my files.
bwa aln -t 4 [...]
bwa samse [...]
bwa samse [...]
Size : About 2 Go
Encoding : Sanger / Illumina 1.9
Total Sequences : about 13 000 000
Sequence length : 51
What can I do to reduce alignment time ? Maybe I should use an other algorithm.
Thanks in advance for your help.
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