新一代测序技术组装拼接软件velvet使用简介.docxVIP

新一代测序技术组装拼接软件velvet使用简介目前用于新一代的测序的主要仪器有Illumina/Solexa的Genome Analyzer、ABI的Solid和Roche的454，它们都能高通量的测序，产生大量的测序结果，接下来就要对序列进行拼接，用于拼接的软件也有很多，比如velvet、soap、abyss、maq等，454的还有专门的newbler。平时用velvet比较多，就简单介绍一下。velvet对短序列的拼接效果比较好，所以多用于对Illumina等产生的短序列片段进行组装拼接。下面以Illumina的GAII产生的结果为例进行说明。一、单端测序单端测序可以直接对fastq格式的原始文件进行处理，首先是用velveth命令建立hash表子集输入./velveth会出来使用帮助：Usage:./velveth directory hash_length {[-file_format][-read_type] filename} [options]directory?????????????? : directory name for output fileshash_length???????????? : odd integer (if even, it will be decremented) = 75 (if above, will be reduced)filename??????????????? : path to sequence file or – for standard inputFile format options:-fasta-fastq-fasta.gz-fastq.gz-eland-geraldRead type options:-short-shortPaired-short2-shortPaired2-long-longPairedOptions:-strand_specific??????? : for strand specific transcriptome sequencing data (default: off)Output:directory/Roadmapsdirectory/Sequences这一步主要是要确定使用的hash值，hash值必须为奇数，且小于MAXKMERLENGTH，这个值默认为31，但是在安装的时候可以调整。具体的命令可以是：velveth result 29 -fastq -short sequence.fastq建立hash子集后用velvetg命令进行组装，输入./velvetg也会出来帮助：Usage:./velvetg directory [options]directory?????????????????????? : working directory nameStandard options:-cov_cutoff floating-point|auto?????? : removal of low coverage nodes AFTER tour bus or allow the system to infer it(default: no removal)-ins_length integer?????????? : expected distance between two paired end reads (default: no read pairing)-read_trkg yes|no???????????? : tracking of short read positions in assembly (default: no tracking)-min_contig_lgth integer????? : minimum contig length exported to contigs.fa file (default: hash length * 2)-amos_file yes|no???????????? : export assembly to AMOS file (default: no export)-exp_cov floating point|auto? : expected coverage of unique regions or allow the system to infer it(default: no long or paired-end read resolution)Advanced options:-ins_length2 integer????????? : expected distance between two paired-end reads in the sec