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  • Assembly stats (reads assembled) from SOAPdenovo

    Hi all,

    I'm trying to get some assembly stats from some SOAPdenovo output - specifically number of reads from the fastq files that were incorporated into the assembly (and maybe how many were ignored, too short, etc). Also, I inherited this data so I'm not completely familiar with SOAPdenovo, but my understanding is that SOAPdenovo doesn't provide SAM output.

    I do, however, have an intermediate outputs folder that contains files such as *.Arc, *.edge, *.newContigIndex, etc. and a statistics folder that contains contig, gap filling, and scaffold info.

    Any suggestions on how to find the number of reads from the fastq files that were incorporated into the final assembly?

    Thanks for any feedback.

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