w2rap-contigger安装及使用

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w2rap-contigger安装及使用

An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.

http://bioinfologics.github.io/the-w2rap-contigger/

一、安装

Pre-requisites

Cmake 2.8.0+
GCC 5.2.0+ (you can also use ICC)
(Optional) jemalloc or another malloc library (intel’s work too).

git clone https://github.com/gonzalogacc/w2rap-contigger.gitcd w2rap-contiggercmake -D CMAKE_CXX_COMPILER=g++ .  make -j 4

二、运行

Example run with input fastq files, K=260 dumping all intermediate files:

mkdir test_k260#optionally, remember to set MALLOC_PER_THREAD and/or OMP_PROC_BINDexport OMP_PROC_BIND=spreadexport MALLOC_PER_THREAD=1./w2rap-contigger -o test_k260 -p example -r -K 260 -t 20 -m 400 M27850_L1_1_clean.fq.gz,M27850_L1_2_clean.fq.gz,M27850_L2_1_clean.fq.gz,M27850_L2_2_clean.fq.gz,M27850_L3_1_clean.fq.gz,M27850_L3_2_clean.fq.gz,M27850_L4_1_clean.fq.gz,M27850_L4_2_clean.fq.gz,M27850_L7_1_clean.fq.gz,M27850_L7_2_clean.fq.gz --to_step 1

擦，剩下的在服务器上运行不了，先作罢。

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