I have used Abyss and then Trans-abyss for a de novo transcriptome assembly with ~70 million reads on a machine with 20gb RAM. From what I've read Abyss is less RAM-intensive than other Trinity and SOAPdenovo. And the memory-intensive phase for Abyss and other assemblers is loading the hash table, which depends on the kmer size, not the number of reads. For these reasons I don't think memory is your issue. Your issue about a large number of duplicate reads specific to one pair of reads and not the other sounds like a possible issue--Abyss has issues when coverage is too high, for example. The Abyss support group is probably a good place to turn. https://groups.google.com/forum/?fro...um/abyss-users
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From my experience MIRA performs very well on de novo tanscriptome assembliesComment
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Trinity-duplicate removal
Dear All,
I am using trinity for transcriptomics assembly. I have few queries:-
1) have two condition(Control and Treated) and each condition has 4 replicates. so if I merge these .fq files together, how the generated assembly from this merged .fq file would be better than the assembly generated from single(using only one replicate) sample?
2) Do I need to remove duplicates from individual fastq file before merging or after merging them together?
3) I saw there is a script "fasta_remove_duplicates" in the trinity folder. So is there any chance that "In-silico-normalization" in trinity take care of these duplicate reads?
I would appreciate any explanations.Comment
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