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Hi,
From documentatioon it appears that ABySS only can output contigs and scaffolds in fasta. Is there a way to get more detailed assemblies, which list reads that compose contigs? My feeling is that this task is restricted to de novo assemblers that can output sam, bam and other more informative assembly formats. I used 454 newbler, but it discards reads shorter that 75 nt or so (Illumina datasets).
From documentatioon it appears that ABySS only can output contigs and scaffolds in fasta. Is there a way to get more detailed assemblies, which list reads that compose contigs? My feeling is that this task is restricted to de novo assemblers that can output sam, bam and other more informative assembly formats. I used 454 newbler, but it discards reads shorter that 75 nt or so (Illumina datasets).