Does it support fa.gz as the input?

[X-WJ]

Well,I have some corrected ont data and i compressed it for saving the storage.And now ,can I use the gz file as the input data ? I don't know the function of "wtpre"?Can I modify the mak file and skip the "wtpre" step? my mak file like this .

PREFIX=species
2
3 EXE_PRE=/smartdenovo/wtpre
4 EXE_ZMO=/smartdenovo/wtzmo
5 EXE_OBT=/smartdenovo/wtobt
6 EXE_GBO=/smartdenovo/wtgbo
7 EXE_CLP=/smartdenovo/wtclp
8 EXE_LAY=/smartdenovo/wtlay
9 EXE_CNS=/smartdenovo/wtcns
10 N_THREADS=20
11
12 all:$(PREFIX).dmo.lay
13 #$(PREFIX).fa.gz:
14 # $(EXE_PRE) -J 5000 species.correctedReads.fasta.gz | gzip -c -1 > $@
15
16 $(PREFIX).dmo.ovl:$(PREFIX).fa.gz
17 $(EXE_ZMO) -t $(N_THREADS) -i $(PREFIX).fa.gz -fo $@ -k 21 -z 10 -Z 16 -U -1 -m 0.1 -A 1000
18
19 $(PREFIX).dmo.obt:$(PREFIX).fa.gz $(PREFIX).dmo.ovl
20 $(EXE_CLP) -i $(PREFIX).dmo.ovl -fo $@ -d 3 -k 300 -m 0.1 -FT
21
22 $(PREFIX).dmo.lay:$(PREFIX).fa.gz $(PREFIX).dmo.obt $(PREFIX).dmo.ovl
23 $(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

Thank you fo reply

[ruanjue]

It's ok.

[X-WJ]

Thank you very much !!

[X-WJ]

It's ok.

Emmc, I have run the smartdenovo the whole pipleline on the other project while it's still running well .And I use the fa.gz as the original input ,not motify the mak file .Deos it fit too ?

[ruanjue]

All program used the same API to read sequences, wtpre can take gz file as input.