deletions | additions       diff --git a/assembly.mk b/assembly.mk  new file mode 100644  index 0000000..b9c989b  --- /dev/null  +++ b/assembly.mk 
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#!/usr/bin/make -rRsf  ###########################################  ### -usage 'assembly.mk RUN=run CPU=8 MEM=15 READ1=/location/of/read1.fastq READ2=/location/of/read2.fastq'  ### -RUN= name of run  ###  ############################################  all:$(CURDIR)/10M_corr/10M.ec.P2/Trinity.fasta \  $(CURDIR)/20M_corr/10M.ec.P2/Trinity.fasta \  $(CURDIR)/50M_corr/10M.ec.P2/Trinity.fasta \  $(CURDIR)/75M_corr/10M.ec.P2/Trinity.fasta \  $(CURDIR)/100M_corr/10M.ec.P2/Trinity.fasta \  K=19  samp10 := 10M  $(CURDIR)/$(samp10)_corr/$(samp10).ec.P2/Trinity.fasta:\  $(CURDIR)/$(samp10)_corr/$(samp10)_corrk19.1.corrected.fastq.gz $(CURDIR)/$(samp10)_corr/$(samp10)_corrk19.2.corrected.fastq.gz  Trinity --seqType fq --JM 50G --trimmomatic \  --left $< \  --right $(word 2,$^) \  --CPU 24 --output $(samp10).ec.P2 \  --quality_trimming_params "ILLUMINACLIP:$(CURDIR)/barcodes.fa:2:40:15 LEADING:2 TRAILING:2 MINLEN:25"  diff --git a/bless.mk b/bless.mk  index 06cbf08..a601d65 100644  --- a/bless.mk  +++ b/bless.mk 
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bless -kmerlength $(K) -read1 $< -read2 $(word 2,$^) -verify -notrim -prefix $(CURDIR)/$(samp)_corr/$(samp)  gzip $(CURDIR)/$(samp)_corr/$(samp).1.corrected.fastq $(CURDIR)/$(samp)_corr/$(samp).2.corrected.fastq &  samp samp20  := 20M $(CURDIR)/$(samp)_corr/$(samp).1.corrected.fastq.gz $(CURDIR)/$(samp)_corr/$(samp).2.corrected.fastq.gz:\  $(CURDIR)/$(samp)_corr/raw.$(samp).SRR797058_1.fastq $(CURDIR)/$(samp)_corr/raw.$(samp).SRR797058_2.fastq $(CURDIR)/$(samp20)_corr/$(samp20).1.corrected.fastq.gz $(CURDIR)/$(samp20)_corr/$(samp20).2.corrected.fastq.gz:\  $(CURDIR)/$(samp20)_corr/raw.$(samp20).SRR797058_1.fastq $(CURDIR)/$(samp20)_corr/raw.$(samp20).SRR797058_2.fastq  @echo '\n\n'BEGIN ERROR CORRECTION: `date +'%a %d%b%Y %H:%M:%S'`  @echo Results will be in a file named *corrected.fastq.gz  @echo Settings used: bless kmerlength = $(K)  bless -kmerlength $(K) -read1 $< -read2 $(word 2,$^) -verify -notrim -prefix $(CURDIR)/$(samp)_corr/$(samp) $(CURDIR)/$(samp20)_corr/$(samp20)  gzip $(CURDIR)/$(samp)_corr/$(samp).1.corrected.fastq $(CURDIR)/$(samp)_corr/$(samp).2.corrected.fastq $(CURDIR)/$(samp20)_corr/$(samp20).1.corrected.fastq $(CURDIR)/$(samp20)_corr/$(samp20).2.corrected.fastq  & samp samp50  := 50M $(CURDIR)/$(samp)_corr/$(samp).1.corrected.fastq.gz $(CURDIR)/$(samp)_corr/$(samp).2.corrected.fastq.gz:\  $(CURDIR)/$(samp)_corr/raw.$(samp).SRR797058_1.fastq $(CURDIR)/$(samp)_corr/raw.$(samp).SRR797058_2.fastq $(CURDIR)/$(samp50)_corr/$(samp50).1.corrected.fastq.gz $(CURDIR)/$(samp50)_corr/$(samp50).2.corrected.fastq.gz:\  $(CURDIR)/$(samp50)_corr/raw.$(samp50).SRR797058_1.fastq $(CURDIR)/$(samp50)_corr/raw.$(samp50).SRR797058_2.fastq  @echo '\n\n'BEGIN ERROR CORRECTION: `date +'%a %d%b%Y %H:%M:%S'`  @echo Results will be in a file named *corrected.fastq.gz  @echo Settings used: bless kmerlength = $(K)  bless -kmerlength $(K) -read1 $< -read2 $(word 2,$^) -verify -notrim -prefix $(CURDIR)/$(samp)_corr/$(samp) $(CURDIR)/$(samp50)_corr/$(samp50)  gzip $(CURDIR)/$(samp)_corr/$(samp).1.corrected.fastq $(CURDIR)/$(samp)_corr/$(samp).2.corrected.fastq $(CURDIR)/$(samp50)_corr/$(samp50).1.corrected.fastq $(CURDIR)/$(samp50)_corr/$(samp50).2.corrected.fastq  & samp samp75  := 75M $(CURDIR)/$(samp)_corr/$(samp).1.corrected.fastq.gz $(CURDIR)/$(samp)_corr/$(samp).2.corrected.fastq.gz:\  $(CURDIR)/$(samp)_corr/raw.$(samp).SRR797058_1.fastq $(CURDIR)/$(samp)_corr/raw.$(samp).SRR797058_2.fastq $(CURDIR)/$(samp75)_corr/$(samp75).1.corrected.fastq.gz $(CURDIR)/$(samp75)_corr/$(samp75).2.corrected.fastq.gz:\  $(CURDIR)/$(samp75)_corr/raw.$(samp75).SRR797058_1.fastq $(CURDIR)/$(samp75)_corr/raw.$(samp75).SRR797058_2.fastq  @echo '\n\n'BEGIN ERROR CORRECTION: `date +'%a %d%b%Y %H:%M:%S'`  @echo Results will be in a file named *corrected.fastq.gz  @echo Settings used: bless kmerlength = $(K)  bless -kmerlength $(K) -read1 $< -read2 $(word 2,$^) -verify -notrim -prefix $(CURDIR)/$(samp)_corr/$(samp) $(CURDIR)/$(samp75)_corr/$(samp75)  gzip $(CURDIR)/$(samp)_corr/$(samp).1.corrected.fastq $(CURDIR)/$(samp)_corr/$(samp).2.corrected.fastq $(CURDIR)/$(samp75)_corr/$(samp75).1.corrected.fastq $(CURDIR)/$(samp75)_corr/$(samp75).2.corrected.fastq  & samp samp100  := 100M $(CURDIR)/$(samp)_corr/$(samp).1.corrected.fastq.gz $(CURDIR)/$(samp)_corr/$(samp).2.corrected.fastq.gz:\  $(CURDIR)/$(samp)_corr/raw.$(samp).SRR797058_1.fastq $(CURDIR)/$(samp)_corr/raw.$(samp).SRR797058_2.fastq $(CURDIR)/$(samp100)_corr/$(samp100).1.corrected.fastq.gz $(CURDIR)/$(samp100)_corr/$(samp100).2.corrected.fastq.gz:\  $(CURDIR)/$(samp100)_corr/raw.$(samp100).SRR797058_1.fastq $(CURDIR)/$(samp100)_corr/raw.$(samp100).SRR797058_2.fastq  @echo '\n\n'BEGIN ERROR CORRECTION: `date +'%a %d%b%Y %H:%M:%S'`  @echo Results will be in a file named *corrected.fastq.gz  @echo Settings used: bless kmerlength = $(K)  bless -kmerlength $(K) -read1 $< -read2 $(word 2,$^) -verify -notrim -prefix $(CURDIR)/$(samp)_corr/$(samp) $(CURDIR)/$(samp100)_corr/$(samp100)  gzip $(CURDIR)/$(samp)_corr/$(samp).1.corrected.fastq $(CURDIR)/$(samp)_corr/$(samp).2.corrected.fastq $(CURDIR)/$(samp100)_corr/$(samp100).1.corrected.fastq $(CURDIR)/$(samp100)_corr/$(samp100).2.corrected.fastq  & #samp := 10M  #Trinity.fasta:$(samp)_corrk19.1.corrected.fastq.gz $(samp)_corrk19.2.corrected.fastq.gz  diff --git a/normalize.mk b/normalize.mk  index 3a93d41..918a0e0 100644  --- a/normalize.mk  +++ b/normalize.mk 
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C=50  NORM_K=25  samp samp10  := 10M $(CURDIR)/$(samp)_corr/$(samp).corr.inter.norm.fastQ:$(CURDIR)/$(samp)_corr/$(samp)_corrk19.1.corrected.fastq.gz $(CURDIR)/$(samp)_corr/$(samp)_corrk19.2.corrected.fastq.gz $(CURDIR)/$(samp10)_corr/$(samp10).corr.inter.norm.fastQ:\  $(CURDIR)/$(samp10)_corr/$(samp10)_corrk19.1.corrected.fastq.gz $(CURDIR)/$(samp10)_corr/$(samp10)_corrk19.2.corrected.fastq.gz  @echo '\n\n'BEGIN NORMALIZATION for $(samp): $(samp10):  `date +'%a %d%b%Y %H:%M:%S'` @echo Settings used: normalize-by-median.py -p -k $(NORM_K) -C $(C) -N 4 -x 15e9  interleave-reads.py $^ -o $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ $(CURDIR)/$(samp10)_corr/$(samp10).corr.inter.fastQ  normalize-by-median.py -p -k $(NORM_K) -C $(C) -N 4 -x 15e9 --out $@ $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ $(CURDIR)/$(samp10)_corr/$(samp10).corr.inter.fastQ  gzip $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ $(CURDIR)/$(samp10)_corr/$(samp10).corr.inter.fastQ  & samp samp20  := 20M $(CURDIR)/$(samp)_corr/$(samp).corr.inter.norm.fastQ:$(CURDIR)/$(samp)_corr/$(samp)_corrk19.1.corrected.fastq.gz $(CURDIR)/$(samp)_corr/$(samp)_corrk19.2.corrected.fastq.gz $(CURDIR)/$(samp20)_corr/$(samp20).corr.inter.norm.fastQ:\  $(CURDIR)/$(samp20)_corr/$(samp20)_corrk19.1.corrected.fastq.gz $(CURDIR)/$(samp20)_corr/$(samp20)_corrk19.2.corrected.fastq.gz  @echo '\n\n'BEGIN NORMALIZATION for $(samp): $(samp20):  `date +'%a %d%b%Y %H:%M:%S'` @echo Settings used: normalize-by-median.py -p -k $(NORM_K) -C $(C) -N 4 -x 15e9  interleave-reads.py $^ -o $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ $(CURDIR)/$(samp20)_corr/$(samp20).corr.inter.fastQ  normalize-by-median.py -p -k $(NORM_K) -C $(C) -N 4 -x 15e9 --out $@ $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ $(CURDIR)/$(samp20)_corr/$(samp20).corr.inter.fastQ  gzip $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ $(CURDIR)/$(samp20)_corr/$(samp20).corr.inter.fastQ  & samp samp50  := 50M $(CURDIR)/$(samp)_corr/$(samp).corr.inter.norm.fastQ:$(CURDIR)/$(samp)_corr/$(samp)_corrk19.1.corrected.fastq.gz $(CURDIR)/$(samp)_corr/$(samp)_corrk19.2.corrected.fastq.gz $(CURDIR)/$(samp50)_corr/$(samp50).corr.inter.norm.fastQ:\  $(CURDIR)/$(samp50)_corr/$(samp50)_corrk19.1.corrected.fastq.gz $(CURDIR)/$(samp50)_corr/$(samp50)_corrk19.2.corrected.fastq.gz  @echo '\n\n'BEGIN NORMALIZATION for $(samp): $(samp50):  `date +'%a %d%b%Y %H:%M:%S'` @echo Settings used: normalize-by-median.py -p -k $(NORM_K) -C $(C) -N 4 -x 15e9  interleave-reads.py $^ -o $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ $(CURDIR)/$(samp50)_corr/$(samp50).corr.inter.fastQ  normalize-by-median.py -p -k $(NORM_K) -C $(C) -N 4 -x 15e9 --out $@ $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ $(CURDIR)/$(samp50)_corr/$(samp50).corr.inter.fastQ  gzip $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ $(CURDIR)/$(samp50)_corr/$(samp50).corr.inter.fastQ  & samp samp75  := 75M $(CURDIR)/$(samp)_corr/$(samp).corr.inter.norm.fastQ:$(CURDIR)/$(samp)_corr/$(samp)_corrk19.1.corrected.fastq.gz $(CURDIR)/$(samp)_corr/$(samp)_corrk19.2.corrected.fastq.gz $(CURDIR)/$(samp75)_corr/$(samp75).corr.inter.norm.fastQ:\  $(CURDIR)/$(samp75)_corr/$(samp75)_corrk19.1.corrected.fastq.gz $(CURDIR)/$(samp75)_corr/$(samp75)_corrk19.2.corrected.fastq.gz  @echo '\n\n'BEGIN NORMALIZATION for $(samp): $(samp75):  `date +'%a %d%b%Y %H:%M:%S'` @echo Settings used: normalize-by-median.py -p -k $(NORM_K) -C $(C) -N 4 -x 15e9  interleave-reads.py $^ -o $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ $(CURDIR)/$(samp75)_corr/$(samp75).corr.inter.fastQ  normalize-by-median.py -p -k $(NORM_K) -C $(C) -N 4 -x 15e9 --out $@ $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ $(CURDIR)/$(samp75)_corr/$(samp75).corr.inter.fastQ  gzip $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ $(CURDIR)/$(samp75)_corr/$(samp75).corr.inter.fastQ  & samp := 100M  $(CURDIR)/$(samp)_corr/$(samp).corr.inter.norm.fastQ:$(CURDIR)/$(samp)_corr/$(samp)_corrk19.1.corrected.fastq.gz $(CURDIR)/$(samp)_corr/$(samp).corr.inter.norm.fastQ:\  $(CURDIR)/$(samp)_corr/$(samp)_corrk19.1.corrected.fastq.gz  $(CURDIR)/$(samp)_corr/$(samp)_corrk19.2.corrected.fastq.gz @echo '\n\n'BEGIN NORMALIZATION for $(samp): `date +'%a %d%b%Y %H:%M:%S'`  @echo Settings used: normalize-by-median.py -p -k $(NORM_K) -C $(C) -N 4 -x 15e9  interleave-reads.py $^ -o $(CURDIR)/$(samp)_corr/$(samp).corr.inter.fastQ