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* The clipped out sequences are recorded in the file of '''clip_out''' |
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* The clipped out sequences are recorded in the file of '''clip_out''' |
| - |
* The unalignable gaps are recorded in the file of '''Gaps''', and the gaps of larger than 95th quantile (R2_gap=0.95) are clipped.
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+ |
* The unalignable gaps are recorded in the file of '''Gaps''', and the size of gaps larger than 95th quantile (R2_gap=0.95) are clipped.
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+ |
* The misassembled contigs recorded in the file of '''Remove_Info''' are removed and extra contigs are introduced if necessary.
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+ |
: For example, in the case of E. coli:
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+ |
: 1 14641 | 36367 21727 | 14641 14641 | 99.99 | CLC_100_len:33932 Abyss_133_len:170886
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+ |
: 14608 33932 | 58206 38882 | 19325 19325 | 100.00 | CLC_100_len:33932 Abyss_129_len:72302
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+ |
: 1 14641 | 31800 17160 | 14641 14641 | 99.99 | CLC_100_len:33932 Edena_65_len:79603
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+ |
: 14608 33932 | 58206 38882 | 19325 19325 | 100.00 | CLC_100_len:33932 Edena_51_len:126254
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+ |
: 1 14641 | 31804 17164 | 14641 14641 | 99.99 | CLC_100_len:33932 Velvet_45_len:70264
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+ |
: 14608 33932 | 13945 33269 | 19325 19325 | 100.00 | CLC_100_len:33932 Velvet_42_len:58831
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+ |
: The representative contig CLC_100 is misassembled. We removed this contig and introduce an extra representative contig - Abyss_129.
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