????1. ?????????????????NGS??????????
????????????????????????????????????????????????????
????1.1 QC(reads??????????)
????Quality Control?????????????reads??????????reads??????????
????????Primer/Adaptor??reads
???????й???non-ATCG???N??reads
???????????????????????????????reads
???????????Щreads?????????????????????????????
????1.2 ??reads????trim????
??????????л??????????????????иò??衣?????????????????????????????ò??衣
???????????3′??????reads????trim????????reads?е??????????????????trim??read????????????????????????????read??
????2. NGS?????QC???
????2.1 NGSQC toolkit
???????????citation:Patel RK?? Jain M (2012). NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS ONE?? 7(2): e30619.
????????????????http://www.nipgr.res.in/ngsqctoolkit.html
???????????????????4??????к?1??PDF?????manual?????manual???????????????4????????ж??????perl??д??????QC?????????????????????????????￡?
????2.1.1 QC??????а?????4?PERL????????454 READS??ILLUMINA READS??QC????????
????IlluQC.pl ????Illumina reads??QC??????????????????primer/adaptor??reads?????????reads???????????????6????ν??????????? (‘-s’ ????) ???????????20????????????????????? ( ‘-l’ ????)???????????reads?б??? >30% ?????????reads???????????????
????$ perl $NGSQCHome/QC/IlluQC_PRLL.pl -pe r1.fq r2.fq 2 5 -p 8 -l 70 -s 20
????IlluQC_PRLL.pl ?????????????ж???????????? ‘-c’ ?????????в??м??????????????
????454QC.pl ??454 reads????QC??
????454QC_PRLL.pl ??????????????????????? ‘-c’ ?????????в??м??????????????
????454QC_PE.pl ??paired-end?????454 reads????QC??
????2.1.2 TRIMINGREADS????а???3?????????READS??TRIMMING????????
????AmbiguityFiltering.pl ?????non-ATCG??reads????trimming???????4??(4?1)trim???????????non-ATCG???????????non-ATCG????(????????)????5′??trim???N?????У???3′??trim???N?????С???????????????????????????reads??cutoff???
????$ perl $NGSQCHome/Trimming/AmbiguityFiltering.pl -i r1.fq -irev r2.fq -p 2 -n 50
????TrimmingReads.pl ??3??(3?1)trim????????????read??5′??trim????????????????????reads??3′??trim????????????????3′??trim??????????????????(???????￡?????????????????????????????reads??cutoff???
????$ perl $NGSQCHome/Trimming/TrimmingReads.pl  -i r1.fq -irev r2.fq -q 13 -n 50
????HomopolymerTrimming.pl
????2.1.3 STATISTICS???????2????????????N50????
????N50Stat.pl ???????fasta?????N50
????AvgQuality.pl ???????454?????reads????
????2.1.4 FORMT-CONVERTER??????г???????????????????????????к???4??PERL??????????
????FastqTo454.pl??FastqToFasta.pl??SangerFastqToIlluFastq.pl??SolexaFastqToIlluFastq.pl??