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A file named [[Media:maia_assembly.fa|maia_assembly.fa]] was generated, containing a draft genome of 4640055 bp with 126761 uncalled bases (Ns). We split the genome into contigs (at >10Ns) and got the set of contigs [[Media: maia.fa|maia.fa]]. |
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A file named [[Media:maia_assembly.fa|maia_assembly.fa]] was generated, containing a draft genome of 4640055 bp with 126761 uncalled bases (Ns). We split the genome into contigs (at >10Ns) and got the set of contigs [[Media: maia.fa|maia.fa]]. |
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<table border=1>
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[[Media:Ecoli.36.m2_gaa.tar.gz|All_M2_GAA]]<br>
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<tr>
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Beacuase minimus2 and GAA merge two assemblies at a time, we iteratively integrate the four assemblies in random order.<br>
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<td>'''''Input'''''</td><td>'''''Download'''''</td>
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minimus2: C_S_V_A_E, A_C_V_S_E, S_V_E_C_A, A_E_C_V_S, A_E_S_C_V, E_V_S_C_A, E_V_C_A_S, V_E_S_A_C, V_S_E_A_C, A_E_V_C_S<br>
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</tr>
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GAA: E_S_C_V_A, V_S_E_C_A, V_S_C_E_A, S_V_C_E_A, V_E_A_S_C, E_C_V_S_A, V_A_S_C_E, V_C_E_S_A, A_S_C_V_E, S_C_V_E_A
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<tr><td>Set1</td><td>[[Media:minimus2.fasta|minimus2_Set1(A,C,E,S,V)]]</td></tr>
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<tr><td>Set1</td><td>[[Media:minimus2(2).fasta|minimus2_Set1(S,C,V,E,A)]]</td></tr>
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Since minimus2 can only merge two sequence sets at a time, we used minimus2 to integrate the set1 in alphabetical order (i.e., ACESV) and in descending order of contig number (i.e., SCEVA).
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After formatting the contig names in the format of >Contig1.1, we conducted GAA to integrate the assembly of Abyss with the assembly of Edena by using the following script and got the set of contigs [[Media: gaa2.fa|gaa2.fa]].
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perl gaa.pl -t ../Abyss_contigs_1.fa -q ../CLC_1.fa -o AC
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Similarly, we can iteratively integrate the output assembly with another assembly to get the set of contigs [[Media:gaa5.fa|gaa5.fa]] (A+C+E+S+V).
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