Hi There,
I have been using Ray to de novo assembly.
The input reads are a mix of illumina pair-end reads (this account for
90%), illumina single-end reads and 454 single end reads.
The command i used is
mpiexec -n 60 Ray \
-i \
/home/s4196896/mix_assembly/input/t15c15/gs1.shuffled.fasta.gz \
-i \
/home/s4196896/mix_assembly/input/t15c15/gs2.shuffled.fasta.gz \
-i \
/home/s4196896/mix_assembly/input/t15c15/gs3.shuffled.fasta.gz \
-s \
/home/s4196896/mix_assembly/input/t15c15/gs2.single.fasta.gz \
-s \
/home/s4196896/mix_assembly/input/t15c15/gs3.single.fasta.gz \
-s \
/home/s4196896/mix_assembly/input/t15c15/gs1.single.fasta.gz \
-s \
/home/s4196896/mix_assembly/input/radseq1.seeds.fasta \
-s \
/home/s4196896/mix_assembly/input/radseq_v2.fasta \
-s \
/work1/s4196896/454_assembly/raw_reads/all_genomic_reads.short.fasta \
-s \
/work1/s4196896/454_assembly/raw_reads/all_genomic_reads.long.fasta \
-o \
71 \
-k \
71
The output shows that scaffolds and contigs are the same (same N50, total
number of bases and number of sequences etc.).
This confused me.
I hope someone can help me out.
Thanks in advance.
Kind Regards,
--
Huanle
School of biological Sciences, UQ, QLD, AU
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