Hi everyone,
I am doing transcriptome assembly on short Illumina reads (both single end and paired end with avg length of 100 bp).
I use different transcriptome assemblers, like MIRA, Velvet Oases, SOAPdenovoTrans.
The avg contig length I got varies from 400 to 1000 bp.
I tried different parameters, like different kmer and different min contig size, but the result does not improve a lot.
I am interested in making much longer contigs (few thousands), so I was wondering is there any way how can I improve and increase this current contig length.
Also, I would like to know why this length varies a lot between different transcriptome assemblers (there is a huge difference between length 400 and length 1000).
I know that Velvet and SOAPdenovo are based on de Bruijn graphs, while MIRA is OLC based.
I would appreciate a lot if someone can share some similar experience with me.
Thank you very much,
Best Regards,
Natasha
I am doing transcriptome assembly on short Illumina reads (both single end and paired end with avg length of 100 bp).
I use different transcriptome assemblers, like MIRA, Velvet Oases, SOAPdenovoTrans.
The avg contig length I got varies from 400 to 1000 bp.
I tried different parameters, like different kmer and different min contig size, but the result does not improve a lot.
I am interested in making much longer contigs (few thousands), so I was wondering is there any way how can I improve and increase this current contig length.
Also, I would like to know why this length varies a lot between different transcriptome assemblers (there is a huge difference between length 400 and length 1000).
I know that Velvet and SOAPdenovo are based on de Bruijn graphs, while MIRA is OLC based.
I would appreciate a lot if someone can share some similar experience with me.
Thank you very much,
Best Regards,
Natasha
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