Generate consensus fasta file with Smartdenovo

[a-velt]

Dear developpers,

First, thank you for your great tool, smartdenovo.

I launched this tools, which is very fast, awesome.

In your documentation, you said to run the following commands :

/path/to/smartdenovo/smartdenovo.pl -p prefix reads.fa > prefix.mak
make -f prefix.mak

That’s what I did but I don’t get a « .cns » file and I don’t have any lines that generate it in my make file.

My make file :

PREFIX=GW_smartdenovo

EXE_PRE=/path/to/smartdenovo/wtpre EXE_ZMO=/path/to/smartdenovo/wtzmo EXE_OBT=/path/to/smartdenovo/wtobt EXE_GBO=/path/to/smartdenovo/wtgbo EXE_CLP=/path/to/smartdenovo/wtclp EXE_LAY=/path/to/smartdenovo/wtlay EXE_CNS=/path/to/smartdenovo/wtcns N_THREADS=10

all:$(PREFIX).dmo.lay

$(PREFIX).fa.gz: $(EXE_PRE) -J 5000 raw_reads.GW.fasta | gzip -c -1 > $@

$(PREFIX).dmo.ovl:$(PREFIX).fa.gz $(EXE_ZMO) -t $(N_THREADS) -i $(PREFIX).fa.gz -fo $@ -k 16 -z 10 -Z 16 -U -1 -m 0.1 -A 1000

$(PREFIX).dmo.obt:$(PREFIX).fa.gz $(PREFIX).dmo.ovl $(EXE_CLP) -i $(PREFIX).dmo.ovl -fo $@ -d 3 -k 300 -m 0.1 -FT

$(PREFIX).dmo.lay:$(PREFIX).fa.gz $(PREFIX).dmo.obt $(PREFIX).dmo.ovl $(EXE_LAY) -i $(PREFIX).fa.gz -b $(PREFIX).dmo.obt -j $(PREFIX).dmo.ovl -fo $(PREFIX).dmo.lay -w 300 -s 200 -m 0.1 -r 0.95 -c 1

My outputs :

GW_smartdenovo.dmo.lay GW_smartdenovo.dmo.lay.1.dot GW_smartdenovo.dmo.lay.2.dot GW_smartdenovo.dmo.lay.3.dot GW_smartdenovo.dmo.lay.4.dot GW_smartdenovo.dmo.lay.5.dot GW_smartdenovo.dmo.lay.contained_reads GW_smartdenovo.dmo.lay.dup GW_smartdenovo.dmo.lay.lnk GW_smartdenovo.dmo.lay.utg GW_smartdenovo.dmo.lay.utg.dup GW_smartdenovo.dmo.obt GW_smartdenovo.dmo.ovl GW_smartdenovo.dmo.ovl.contained GW_smartdenovo.fa.gz GW_smartdenovo.mak

Is it the file « .dmo.lay.utg » that is the final assembly ? Was there a polishing step ? Knowing that I have « quiver » available on the server on which I launched smartdenovo.

Thank you for your response. Best, Amandine

[ruanjue]

/path/to/smartdenovo/smartdenovo.pl -p prefix reads.fa -c 1 > prefix.mak -c 1 will generate the consensus command line

[a-velt]

Dear Jue Ruan,

I launched the command with the -c 1 option and I have the following outputs :

GW_smartdenovo.dmo.lay.utg.dup GW_smartdenovo.dmo.lay.lnk GW_smartdenovo.dmo.lay.utg GW_smartdenovo.dmo.lay.dup GW_smartdenovo.dmo.lay GW_smartdenovo.dmo.lay.5.dot GW_smartdenovo.dmo.lay.4.dot GW_smartdenovo.dmo.lay.3.dot GW_smartdenovo.dmo.lay.2.dot GW_smartdenovo.dmo.lay.contained_reads GW_smartdenovo.dmo.lay.1.dot GW_smartdenovo.dmo.obt GW_smartdenovo.dmo.ovl GW_smartdenovo.dmo.ovl.contained GW_smartdenovo.fa.gz GW_smartdenovo.mak

But no consensus file seems to be here ... Is it normal ?

My make file :

PREFIX=GW_smartdenovo

EXE_PRE=/path/to/smartdenovo/wtpre EXE_ZMO=/path/to/smartdenovo/wtzmo EXE_OBT=/path/to/smartdenovo/wtobt EXE_GBO=/path/to/smartdenovo/wtgbo EXE_CLP=/path/to/smartdenovo/wtclp EXE_LAY=/path/to/smartdenovo/wtlay EXE_CNS=/path/to/smartdenovo/wtcns N_THREADS=10

all:$(PREFIX).dmo.lay

$(PREFIX).fa.gz: $(EXE_PRE) -J 5000 /path/to/raw_reads.GW.fasta | gzip -c -1 > $@

$(PREFIX).dmo.ovl:$(PREFIX).fa.gz $(EXE_ZMO) -t $(N_THREADS) -i $(PREFIX).fa.gz -fo $@ -k 16 -z 10 -Z 16 -U -1 -m 0.1 -A 1000

$(PREFIX).dmo.obt:$(PREFIX).fa.gz $(PREFIX).dmo.ovl $(EXE_CLP) -i $(PREFIX).dmo.ovl -fo $@ -d 3 -k 300 -m 0.1 -FT

$(PREFIX).dmo.lay:$(PREFIX).fa.gz $(PREFIX).dmo.obt $(PREFIX).dmo.ovl $(EXE_LAY) -i $(PREFIX).fa.gz -b $(PREFIX).dmo.obt -j $(PREFIX).dmo.ovl -fo $(PREFIX).dmo.lay -w 300 -s 200 -m 0.1 -r 0.95 -c 1

Best, Amandine

[ruanjue]

I am not sure why smartdenovo.pl -c 1 didn't work. Please run the consensus by yourself.

wtcns -t 10 GW_smartdenovo.dmo.lay > GW_smartdenovo.dmo.cns.fa