Assembly

Denovo assembly (without a reference sequecne)
Assembly (with a reference sequence)

Files:



In [2]:

    
forward = "output_forward_paired.fq.gz"
reverse = "output_reverse_paired.fq.gz"

De novo Assembly



In [4]:









    



Object `%writefile` not found.

Create config file



In [7]:

    
config_file = "soapdenovo.config"



In [9]:

    
%%writefile soapdenovo.config
#maximal read length
max_rd_len=100
[LIB]

#average insert size
avg_ins=200

#if sequence needs to be reversed
reverse_seq=1

#in which part(s) the reads are used
asm_flags=3

#in which order the reads are used while scaffolding
rank=1

# cutoff of pair number for a reliable connection
pair_num_cutoff=2

#fastq file for read 1
q1=forward

#fastq file for read 2 always follows fastq file for read 1
q2=reverse









    



Overwriting soapdenovo.config

SOAPdenovo



In [10]:

    
!/Applications/bioinfo/SOAPdenovo/SOAPdenovo-63mer all -s config_file -K 63 -R -o graph_prefix 1>ass.log 2>ass.err



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