Cannot assemble a simple example
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standage commented
Consider the following 8 reads.
>seq1
ATCCTGAGAATCAATCTGTGAAAATTATGTCTTGGGAGGAGGGGAAGGAAACCAAAAATTTTTAGAAAAGCTGGAACTCTTAGCTATCTAGAAGCAGGTC
>seq2
GGGAAGGAAACCAAAAATTTTTAGAAAAGCTGGAACTCTTAGCTATCTAGAAGCAGGTCTTGAATCTCACAGAATCGCAAAGGAAGAAAATCAGGGCCTA
>seq3
TTTAGAAAAGCTGGAACTCTTAGCTATCTAGAAGCAGGTCTTGAATATCACAGAATCGCAAAGGAAGAAAATCAGGGCCTACCTATCTAAATTTAAAATT
>seq4
GAAATTTTAAATTTAGATATGTAGGCCCTGATTTTCTTCCTTTGCGATTCTGTGATATTCAAGACCTGCTTCTAGATAGCTAAGAGTTCCAGCTTTTCTA
>seq5
TGAGAAAATTATGTCTTGGGAGGAGGGGAAGGAAACCAAAAATTTTTAGAAAAGCTGGAACTCTTAGCTATCTAGAAGCAGGTCTTGAATATCACAGAAT
>seq6
TGAAAATTATGTCTTGGGAGGAGGGGAAGGAAACCAAAAATTTTTAGAAAAGCTGGAACTCTTAGCTATCTAGAAGCAGGTCTTGAATATCACAGAATCG
>seq7
TTTTTAGAAAAGCTGGAACTCTTAGCTATCTAGAAGCAGGTCTTGAATATCACAGAATCGCAAAGGAAGAAAATCAGGGCCTACATATCTAAATTTAAAA
>seq8
ATAGCTAAGAGTTCCAGCTTTTCTAAAAATTTTTGGTTTCCTTCCCCTCCTCCCAAGACATAATTTTCACAGATTGATTCTCAGGATTGGCAATCATGCA
A quick multiple sequence alignment shows that there is very good consensus among these 8 reads for most of the alignment.
seq1 -------------atcctgagaatcaatctgtgaaaattatgtcttgggaggaggggaag
_R_seq8 tgcatgattgccaatcctgagaatcaatctgtgaaaattatgtcttgggaggaggggaag
seq5 -----------------------------tgagaaaattatgtcttgggaggaggggaag
seq6 -------------------------------tgaaaattatgtcttgggaggaggggaag
seq2 ------------------------------------------------------gggaag
seq3 ------------------------------------------------------------
_R_seq4 ------------------------------------------------------------
seq7 ------------------------------------------------------------
seq1 gaaaccaaaaatttttagaaaagctggaactcttagctatctagaagcaggtc-------
_R_seq8 gaaaccaaaaatttttagaaaagctggaactcttagctat--------------------
seq5 gaaaccaaaaatttttagaaaagctggaactcttagctatctagaagcaggtcttgaata
seq6 gaaaccaaaaatttttagaaaagctggaactcttagctatctagaagcaggtcttgaata
seq2 gaaaccaaaaatttttagaaaagctggaactcttagctatctagaagcaggtcttgaatc
seq3 -------------tttagaaaagctggaactcttagctatctagaagcaggtcttgaata
_R_seq4 ---------------tagaaaagctggaactcttagctatctagaagcaggtcttgaata
seq7 -----------tttttagaaaagctggaactcttagctatctagaagcaggtcttgaata
*************************
seq1 -------------------------------------------------------
_R_seq8 -------------------------------------------------------
seq5 tcacagaat----------------------------------------------
seq6 tcacagaatcg--------------------------------------------
seq2 tcacagaatcgcaaaggaagaaaatcagggccta---------------------
seq3 tcacagaatcgcaaaggaagaaaatcagggcctacctatctaaatttaaaatt--
_R_seq4 tcacagaatcgcaaaggaagaaaatcagggcctacatatctaaatttaaaatttc
seq7 tcacagaatcgcaaaggaagaaaatcagggcctacatatctaaatttaaaa----
However, I cannot get fml-asm
to produce any assembly from these reads. I've tried relaxing parameters in various ways but with no success. Are there any parameter settings that will assemble these reads, or is this a particularly challenging case that can't easily be solved?
Thanks!