試用感想:
畫面不錯，安裝時需注意，安裝路徑不可有中文，不然不能執行。在linux和mac上，demo會出不來。
大一點的檔案會跑出現"java.lang.StringIndexOutOfBoundsException: String index out of range:3573470"的錯誤訊息。
如果你的read數較少，這會是不錯的工具，read數較多，也許就不太適用了。
inGAP is an integrated platform for
next-generation sequencing project, the core function of which is to
detect SNPs and indels using a Bayesian algorithm.
(1) It does not
have any read length restriction. It can handle 454 sequencing and/or
Illumina Solexa sequencing and/or Sanger sequencing data sets.
(2)
It can detect most small indels in either single-end or paired-end data
sets. Using the simulated data sets, inGAP could successfully identify
85%-98% of small indels with high accuracy (>99%).
(3) It has a
strong capability to identify variants based on a relatively divergent
reference genome, which bring it to a much wider application other than
resequencing projects.
(4) It provides a user-friendly graphic
interface, through which users can browse, search, check, classify, and
even edit the identified variants.
(5) It can be used to detect
intraspecific polymorphisms (including SNPs and indels) based on a
pairwise comparison of multiple whole genomes.
(6) It employs a global heuristic searching approach to layout contigs based on one or more reference genomes.
(7) It also provides a handful of bioinformatic tools for read simulation, mutation incorporation, format conversion, etc.
(8) It's slower
than other SNP detection programs (e.g. MAQ, SOAP, Bowtie), because it
employs BLAST or BLAT to map reads. It takes ~220 minutes to map 10
million 76bp Illumina reads to a 12Mb yeast genome on an 8-core DELL
machine.
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