ruanjue/wtdbg

A fuzzy Bruijn graph approach to long noisy reads assembly

wtdbg

A fuzzy Bruijn graph (FBG) approach to long noisy reads assembly

wtdbg is desiged to assemble huge genomes in very limited time, it requires a PowerPC with multiple-cores and very big RAM (1Tb+). wtdbg can assemble a 100 X human pacbio dataset within one day.

Assembly of big genomes using PacBio data

# assembly of contigs
wtdbg-1.1.006 -t 96 -i pb-reads.fa -o dbg -H -k 21 -S 1.02 -e 3 2>&1 | tee log.wtdbg
# -t: number of threads, please type 'wtdbg-1.1.006 -h' to get a document
# -i: you can set more than one sequences files, such as -i 1.fa. -i 2.fq -i 3.fa.gz -i 4.fq.gz
# -o: the prefix of results
# -S: 1.01 will use all kmers, 1.02 will use half by sumsampling, 1.04 will use 1/4, and so on
#     2.01 will use half by picking minimizers, but not fully tested
# -e: if too low coverage(< 30 X), try to set -e 2
# please note that dbg.ctg.fa is full of errors from raw reads

# first round of polishment
wtdbg-cns -t 96 -i dbg.ctg.lay -o dbg.ctg.lay.fa -k 15 2>&1 | tee log.cns.1
# dbg.ctg.lay.fa is the polished contigs

# if possible, further polishment
minimap -t 96 -L 100 dbg.ctg.lay.fa pb-reads.fa 2> >(tee log.minimap) | best_minimap_hit.pl | awk '{print $6"\t"$8"\t"$9"\t"$1"\t"$5"\t"$3"\t"$4}' >dbg.map
map2dbgcns dbg.ctg.lay.fa pb-reads.fa dbg.map >dbg.map.lay
wtdbg-cns -t 96 -i dbg.map.lay -o dbg.map.lay.fa -k 13 2>&1 | tee log.cns.2
# you need to concat all reads into one file for minimap and map2dbgcns
# dbg.map.lay.fa is the final contigs

Assembly of huge genomes

wtdbg can handle huge genomes (10G+). Test showed that, for 20X PacBio data of a plant genome of 10G bp, contigs can be assembled within one day.

Contact

Jue Ruan [email protected]

wtdbg's Issues

Compilation fails: string.h:51:20: error: expected ‘)’ before ‘VString

I am trying to compile wtdbg and get the following error:

file_reader.c:247:8: note: include ‘<string.h>’ or provide a declaration of ‘strlen’
In file included from list.h:24:0,
from dmo.h:20,
from wtdbg.c:20:
./string.h:51:20: error: expected ‘)’ before ‘VString’
define_list(VStrv, VString);
^
In file included from list.h:24:0,
from dmo.h:20,
from wtdbg.c:20:
./string.h:245:71: error: unknown type name ‘VStrv’
static inline string_size_t split_string(String *str, char separator, VStrv *vstrs){
^
./string.h:270:73: error: unknown type name ‘VStrv’
static inline string_size_t split_vstring(VString *str, char separator, VStrv *vstrs, string_size_t cut){
^
In file included from dmo.h:20:0,
from wtdbg.c:20:

Additionally, there are thousand warning like this:

list.h:341:2: note: include ‘<string.h>’ or provide a declaration of ‘memcpy’
memcpy(list1->buffer + list1->size, ary, sizeof(e_type) * size); \

Probably one should add #include <string.h> to all c files.

GFA output of polished DBG

Would it be easy to add support for GFAv1 output to wtdbg? I'd like to use the polished (and ideally compacted) DBG as input to another process and this would make it easy to do so.

Scaffolding suggestions

Hello,

I used wtdbg to build contigs using Pacbio reads. Do you recommend any particular tools for scaffolding?

Thanks.

Compile problem: CPATH --- make: *** [wtdbg] Error 1

Hello,

I got the following error message when I typed "make":

wtdbg_make_error.txt

Linux version: 2.6.32-504.el6.x86_64
GCC version: 4.9.3
OS: CentOS release 6.6 (Final)

I don't know about C or C++ and don't know what these messages say. Do you know how to fix this? Thanks!

about parameter -k

hello
I want to know how to determine the value of the parameter -k ?

assembly of contigs

hello，
Does the result of this step need to be completed before the program can be output，process files are not generated while the program is running？

Recommendations for more sensitive overlaps?

Hi I am assembling a BAC (~200kbp) using pacbio data that has a large internal duplications (50 kbp) with some sequence differences.

Do you have any suggestions for parameters I could adjust to make overlapping more sensitive/discerning between the two duplications?

Thanks!