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Sorry, current version of metaSPAdes can work either with single library (paired-end only) or in hybrid paired-end + (TSLR or PacBio or Nanopore) mode.
This is slightly confusing as the Single reads are not used in metagenomic mode does not crash the run, but result in the merged files not being used. So if I have fastq files merged using bbmerge.sh, how should I supply them to spades?
Also, doesn't this effect the insert size distribution? after using bbmerge, both the non-merged interleaved output fastq should have all inserts of size 0.
I would appreciate your input on these and if you could explain why multiple libraries are not supported in meta mode.
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Running spades in meta mode, with any of:
--merged
,--pe-m
,--s
results inSingle reads are not used in metagenomic mode
.The docs mention using external software prior to using spades for merging paired end libraries .
The same page also mentions when the merged reads should be supplies as a "SEPARATE single-read library", however trying that reports:
This is slightly confusing as the
Single reads are not used in metagenomic mode
does not crash the run, but result in the merged files not being used. So if I have fastq files merged using bbmerge.sh, how should I supply them to spades?Also, doesn't this effect the insert size distribution? after using bbmerge, both the non-merged interleaved output fastq should have all inserts of size 0.
I would appreciate your input on these and if you could explain why multiple libraries are not supported in meta mode.
Thank you for developing and maintaining Spades!
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