Code:
> AAAAA
Code:
> AAA > AAA > AAA
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> AAAAA
> AAA > AAA > AAA
bbsplit.sh\ -Xmx23g\ averagepairdist=200\ deterministic=t\ k=8\ minid=0.75\ idfilter=0.75\ maxindel=20\ nzo=f\ po=t\ ambiguous2=split\ ref=test_ref\ idtag=t\ in=Input_1P.fastq\ in2=Input_2P.fastq\ outm=Mapped.sam\ outu=Unmapped.sam\
@HD VN:1.4 SO:unsorted @SQ SN:006_Koxy_tonB_PC LN:317 @SQ SN:022_NDM_PC LN:267 @PG ID:BBMap PN:BBMap VN:37.22 CL:java -Djava.library.path=/install/bbmap/jni/ -ea -Xmx23g align2.BBSplitter ow=t fastareadlen=500 minhits=1 minratio=0.56 maxindel=20 qtrim=rl untrim=t trimq=6 -Xmx23g averagepairdist=200 deterministic=t k=8 minid=0.75 idfilter=0.75 maxindel=20 nzo=f po=t ambiguous2=split ref=test_ref idtag=t in=Input_1P.fastq in2=Input_2P.fastq outm=Mapped.sam outu=Unmapped.sam gi|828959694|gb|CP011636.1|_Klebsiella_oxytoca_strain_CAV1374,_complete_genome_(reversed)-1-146 83 006_Koxy_tonB_PC 209 18 4=2X2=37I100= = 6 -311 ATCAAGCTGTTTGCCGGGAATAACAACCAGCGCGGGGCGGCGTTTGACGTTACCGGGGCGCTGGACGATAACGATCGCGTGGCGGCGCGCTTAAGCGGCATGACCCGCTATGCAGACTCGCAGTTTGATACCTTAAAAGAGCAGC ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? NM:i:39 AM:i:18 YI:f:73.10 gi|828959694|gb|CP011636.1|_Klebsiella_oxytoca_strain_CAV1374,_complete_genome_(reversed)-1-146 163 006_Koxy_tonB_PC 6 9 87=1X2=47I1X1=1X3=2X = 209 311 AATGATGGGCGATACCAACTCGCACAGCTCGCTGGTGGTCGATCCGTGGTTCCTGGAAAATATCGAAGTGGTGCGCGGCCCGGCCTCAGTGCTGTACGGCCGCTCTTCGCCCGGCGGCATCGTCGCCCTCACCTCGCGTAAACCC ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? NM:i:52 AM:i:9 YI:f:64.14 gi|828959694|gb|CP011636.1|_Klebsiella_oxytoca_strain_CAV1374,_complete_genome_(reversed)-1-146 83 006_Koxy_tonB_PC 209 18 4=2X2=37I100= = 6 -311 ATCAAGCTGTTTGCCGGGAATAACAACCAGCGCGGGGCGGCGTTTGACGTTACCGGGGCGCTGGACGATAACGATCGCGTGGCGGCGCGCTTAAGCGGCATGACCCGCTATGCAGACTCGCAGTTTGATACCTTAAAAGAGCAGC ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? NM:i:39 AM:i:18 YI:f:73.10 gi|828959694|gb|CP011636.1|_Klebsiella_oxytoca_strain_CAV1374,_complete_genome_(reversed)-1-146 163 006_Koxy_tonB_PC 6 9 87=1X2=47I1X1=1X3=2X = 209 311 AATGATGGGCGATACCAACTCGCACAGCTCGCTGGTGGTCGATCCGTGGTTCCTGGAAAATATCGAAGTGGTGCGCGGCCCGGCCTCAGTGCTGTACGGCCGCTCTTCGCCCGGCGGCATCGTCGCCCTCACCTCGCGTAAACCC ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? NM:i:52 AM:i:9 YI:f:64.14 gi|828959694|gb|CP011636.1|_Klebsiella_oxytoca_strain_CAV1374,_complete_genome_(reversed)-1-146 83 006_Koxy_tonB_PC 209 18 4=2X2=37I100= = 6 -311 ATCAAGCTGTTTGCCGGGAATAACAACCAGCGCGGGGCGGCGTTTGACGTTACCGGGGCGCTGGACGATAACGATCGCGTGGCGGCGCGCTTAAGCGGCATGACCCGCTATGCAGACTCGCAGTTTGATACCTTAAAAGAGCAGC ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? NM:i:39 AM:i:18 YI:f:73.10 gi|828959694|gb|CP011636.1|_Klebsiella_oxytoca_strain_CAV1374,_complete_genome_(reversed)-1-146 163 006_Koxy_tonB_PC 6 9 87=1X2=47I1X1=1X3=2X = 209 311 AATGATGGGCGATACCAACTCGCACAGCTCGCTGGTGGTCGATCCGTGGTTCCTGGAAAATATCGAAGTGGTGCGCGGCCCGGCCTCAGTGCTGTACGGCCGCTCTTCGCCCGGCGGCATCGTCGCCCTCACCTCGCGTAAACCC ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? NM:i:52 AM:i:9 YI:f:64.14
reformat.sh in1=R1.fq in2=R2.fq out=stdout.fq | dedupe.sh in=stdin.fq out=stdout.fq | reformat.sh in=stdin.fq out1=new1.fq out2=new2.fq
dedupe=t optical=f All duplicates are detected, whether optical or not. All copies except one are removed for each duplicate.
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