assemble~platanus

Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.

input_1:paired-end FASTQ

input_1/DRR015801.1M_1.fastq

@DRR015801.1 HWI-ST895:156:C1HNFACXX:1:1101:2347:1967/1
NACATCATCACATCGCTGGGCTGTCTGGAAGGTGGTGACCTGGATATCGCTTATCTTTCTGAAATTGACCCCACCTGGACGGACAGCAGCCTGACCACCA
+
#1:DDDFFHGHHHJJIJJBHIJJIHIJJJIJJ?DGDHIJJJIJIJJJJJJJJJJJJJJJIJIIJHHHHHHFFFDDCEDDDDDDDDDDDDDDDDDDDDDDD
@DRR015801.2 HWI-ST895:156:C1HNFACXX:1:1101:2281:1982/1
NTATCTTGCTATCCCCAAAAAATTCAGAGATGAGTCGAAAGTCATATCTTTCATGTATGATAAGAATAAAACGTATATTTTGCTATTTTTGATTGCTTTT
+
#1=DDFFFHHHHHJJJJJJJJJJJJJJJIIJJIIHIIJIJJEHIJJJIJJJIJJJGIJJJJJIJIJJJJJHHHHFBFFFFEEEEEEEEDD@DDDDDDDDC
@DRR015801.3 HWI-ST895:156:C1HNFACXX:1:1101:2751:1963/1
NAGAAACCTCCTGAGATCACCCTGAAAAGAATAGGAGAGGAGGCGGGTAAAATCTATATGATACAGAGACAACGATGTTCCCGCTGTGGGACACAGCGGG

input_1/DRR015801.1M_2.fastq

@DRR015801.1 HWI-ST895:156:C1HNFACXX:1:1101:2347:1967/2
GCATATTAAAGGCGCTGGCAATGGCATCTGCTGCACAGGCCCCCTGTGCTATCGGATTGGCAAAGATGACAGCTTCCGGATTGAGAATGGTGGTCAGGCT
+
CCCFFFFFHHHGGJIJIJJJJIJJJJIJJIICGGJJIGIJJJIJHIHIIGFGGIJGHHCDEFFECCCECEDCACDDDDDBBB<ACBDDCC4@B5CCDDD@
@DRR015801.2 HWI-ST895:156:C1HNFACXX:1:1101:2281:1982/2
GTGTATGGGCAAATGAAACCATTGAAAAAGCAATCAAAAATAGCAAAATATACGTTTTATTCTTATCATACATGAAAGATATGACTTTCGACTCATCTCT
+
@BCDFFFFHHHHHJJJJJJJJJJIJGJIHGHIJJJJJJJJIJIJJJJIJJHIIIGIJJIJJIJJIIJJJIJJJIHHHHHFFFFFFFFEEDDDDDDDDDDE
@DRR015801.3 HWI-ST895:156:C1HNFACXX:1:1101:2751:1963/2
CAGTCGATCAATAATATTCCACTGGATGCGCGTAATCACGGCTATACGGTGCTGGATATTCAGCAAGACGGGCCGACCATTCGTTATTTAATTCAGAAAT

input_2:mate-pair FASTQ

Option

-c 15 -m 200 input_1/

Output

platanus_gapClosed.fa

>scaffold1_cov18
TACTGTTTGTGCTGGGATGTTTATTCCCTGCATGGTTTGCGTGGTTTGCGTGGATCTTCGGTGCGTTGTGCTGGATGACG
ACCTTTACGCGGGTGTGGAGTGGGTATCTGACGCTGAAGTCGCTCCAGCGTCAGTAATTGCAATGTTATTTGCTACTGTC
CGGGCCGCGTTCACCGGTTGCTACCGGATTTTTTGGATCGCTGCTCCATTCGTACCAGCCGCCGTCGTAAACGGAGACGT
TATTCCAGCCCATGGCGCGTGCGTACATAAAGGTTTCGGACGCGCGCCAGCCGGTGCCGCAGTAGAATGAAACTTGCTGC
TCTGGTTTGATATTCCACGCTTTCCACATAGCGGTAATATCATCGGCGCTGCGCATGGTGCCATCCGGGTTATGAAAATC
TTCCATATGCGTCGAGTCGCTACCAGCGTGTCCCCAACGTGCTCCGGCTATTTCACCTTTTGGTTTAATATAGCTGTAAC
CGCTGGTCGTACCGATAAATTCTGGCCACGAACGAATGCTCACCAGCGATGCATCCTGGCGATGCAGCAGTCCACGGGCC
TGTTCCATATCGAGCATCAACTGCGGTTGTGCCGGGATCTTCACGCCGAAATCCGGTTCCGCTTTCACTTTCGGTGGCGT
TCCTCGCTCAACAGGCAGTCCCGCGTCGGACCAGGTTTGCCAGCCGCCATCCAGCAGACGCACATCTTTCACGCCTGCGT

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