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3.2-Assembly.txt
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#The data is in:
#/home/projects/ku_10004/people/lzepeda/Vampires/DESR/DR_554
#https://sid.erda.dk/wsgi-bin/ls.py?share_id=biik3KGgru
###################### de novo assembly
mkdir /home/manager/Exercises/3.2-Assembly
cd /home/manager/Exercises/3.2-Assembly
gunzip /home/manager/Data/Vampire_dataset/DR_554.cleaned.R*.fastq.gz
fq2fa --filter --paired --merge /home/manager/Data/Vampire_dataset/DR_554.cleaned.R1.fastq /home/manager/Data/Vampire_dataset/DR_554.cleaned.R2.fastq interleaved_DR_554.fa
idba_ud -r interleaved_DR_554.fa -o idba_ud_assembly
######Get your assembly stats
assemblathon_stats.pl idba_ud_assembly/contig-60.fa
######Extra exercises
####Look at SupplFiles/3.2.3-CmndsForRunningTheTestedAssemblers.pdf
#Try them if you want :)
##metaSpades
#nano input.yaml
[ { orientation: "fr", type: "paired-end", left reads: [ "/home/manager/Data/Vampire_dataset/DR_554.cleaned.R1.fastq" ], right reads: [ "/home/manager/Data/Vampire_dataset/DR_554.cleaned.R2.fastq" ] } ]
spades.py -k 21,31,41,51,61,71,81,91,101 --meta --dataset input.yaml -o metaSpades_results
megahit --k-min 21 --k-max 101 --k-step 10 -m 0.2 -1 /home/manager/Data/Vampire_dataset/DR_554.cleaned.R1.fastq -2 /home/manager/Data/Vampire_dataset/DR_554.cleaned.R2.fastq
velveth assemblyVelvet_101 101 -shortPaired -fastq -separate /home/manager/Data/Vampire_dataset/DR_554.cleaned.R1.fastq /home/manager/Data/Vampire_dataset/DR_554.cleaned.R2.fastq
velvetg assemblyVelvet_101 -ins_length 350 -ins_length_sd 200 -exp_cov auto
meta-velvetg assemblyVelvet_101 -ins_length 350 -ins_length_sd 200 -scaffolding yes
mpiexec -H localhost Ray -k 101 -p /home/manager/Data/Vampire_dataset/DR_554.cleaned.R1.fastq /home/manager/Data/Vampire_dataset/DR_554.cleaned.R2.fastq -o assemblyRayMeta
#nano soap2.config
max_rd_len=600[LIB]avg_ins=350reverse_seq=0asm_flags=3rank=1map_len=100pair_num_cutoff=2q1=/home/manager/Data/Vampire_dataset/DR_554.cleaned.R1.fastq
q2=/home/manager/Data/Vampire_dataset/DR_554.cleaned.R2.fastq
/home/manager/Software/SOAPdenovo2/SOAPdenovo-127mer all -o assemblySOAPdenovo -s soap2.config -K 101 -M 3 -d 1 -R -F
####Read and understand supple Files 3.2.1 and 3.2.2 too. Ask questions if in doubt of anything.