diff --git a/docs/gfastats.md b/docs/gfastats.md index 357f5d6..006f824 100644 --- a/docs/gfastats.md +++ b/docs/gfastats.md @@ -1,18 +1,22 @@ +Let's get some test files first: +``` +mv testFiles-gfastats/* . +``` Help: ``` gfastats -h ``` File: ``` -cat testFiles/random1.fasta +cat random1.fasta ``` Summary statistics: ``` -gfastats testFiles/random1.fasta +gfastats random1.fasta ``` Tabular output: ``` -gfastats testFiles/random1.fasta -t +gfastats random1.fasta -t ``` Change locale: ``` @@ -20,115 +24,115 @@ gfastats large_input.fasta.gz --locale en_US.UTF-8 ``` Full output: ``` -gfastats testFiles/random1.fasta --nstar-report +gfastats random1.fasta --nstar-report ``` Report by sequence: ``` -gfastats testFiles/random1.fasta --seq-report +gfastats random1.fasta --seq-report ``` Original file: ``` -gfastats testFiles/random1.fasta -ofa +gfastats random1.fasta -ofa ``` Line length: ``` -gfastats testFiles/random1.fasta -ofa --line-length 2 +gfastats random1.fasta -ofa --line-length 2 ``` Subset: ``` -gfastats testFiles/random1.fasta Header2 -ofa +gfastats random1.fasta Header2 -ofa ``` Subset with bed: ``` -gfastats testFiles/random1.fasta -e <(echo Header2) -ofa +gfastats random1.fasta -e <(echo Header2) -ofa ``` -cat testFiles/random1.fasta.bed` +cat random1.fasta.bed` ``` -gfastats testFiles/random1.fasta -ofa -e testFiles/random1.fasta.bed +gfastats random1.fasta -ofa -e random1.fasta.bed ``` ``` -gfastats testFiles/random1.fasta -ofa -i testFiles/random1.fasta.bed +gfastats random1.fasta -ofa -i random1.fasta.bed ``` Size of components: ``` -gfastats testFiles/random1.fasta -s s +gfastats random1.fasta -s s ``` ``` -gfastats testFiles/random1.fasta -s c +gfastats random1.fasta -s c ``` ``` -gfastats testFiles/random1.fasta -s g +gfastats random1.fasta -s g ``` AGP: ``` -gfastats testFiles/random1.fasta -b a +gfastats random1.fasta -b a ``` BED coordinates: ``` -gfastats testFiles/random1.fasta -b s +gfastats random1.fasta -b s ``` ``` -gfastats testFiles/random1.fasta -b c +gfastats random1.fasta -b c ``` ``` -gfastats testFiles/random1.fasta -b g +gfastats random1.fasta -b g ``` Sorting: ``` -gfastats testFiles/random1.fasta -ofa --sort largest +gfastats random1.fasta -ofa --sort largest ``` ``` -gfastats testFiles/random1.fasta -ofa --sort descending +gfastats random1.fasta -ofa --sort descending ``` ``` -gfastats testFiles/random1.fasta -ofa --sort test.sort +gfastats random1.fasta -ofa --sort test.sort ``` GFA2: ``` -gfastats testFiles/random1.gfa2 -o gfa2 +gfastats random1.gfa2 -o gfa2 ``` GFA2 to FASTA conversion: ``` -gfastats testFiles/random1.gfa2 -o fasta +gfastats random1.gfa2 -o fasta ``` GFA2 to GFA1 conversion: ``` -gfastats testFiles/random1.gfa2 -o gfa +gfastats random1.gfa2 -o gfa ``` GFA1: ``` -gfastats testFiles/random2.gfa -o gfa +gfastats random2.gfa -o gfa ``` GFA1 to FASTA: ``` -gfastats testFiles/random2.gfa -o fasta +gfastats random2.gfa -o fasta ``` GFA1 to GFA2: ``` -gfastats testFiles/random2.gfa -o gfa2 +gfastats random2.gfa -o gfa2 ``` GFA1 no sequence: ``` -gfastats testFiles/random2.noseq.gfa -o gfa +gfastats random2.noseq.gfa -o gfa ``` GFA1 no sequence: ``` -gfastats testFiles/random2.noseq.gfa -o fa +gfastats random2.noseq.gfa -o fa ``` Homopolymer compression: ``` -gfastats testFiles/random1.fasta --homopolymer-compress 1 -ofa +gfastats random1.fasta --homopolymer-compress 1 -ofa ``` Find terminal overlaps: ``` -gfastats testFiles/random5.findovl.gfa -ogfa +gfastats random5.findovl.gfa -ogfa ``` ``` -gfastats testFiles/random5.findovl.gfa --discover-terminal-overlaps 3 -ogfa +gfastats random5.findovl.gfa --discover-terminal-overlaps 3 -ogfa ``` Discover paths: ``` -gfastats testFiles/random1.fasta -ogfa | grep -v "^P" > test.gfa +gfastats random1.fasta -ogfa | grep -v "^P" > test.gfa ``` ``` gfastats test.gfa -ogfa @@ -138,32 +142,32 @@ gfastats test.gfa -ogfa2 --discover-paths ``` Superimpose AGP: ``` -gfastats testFiles/random1.fasta -a testFiles/random1.agp -ofa +gfastats random1.fasta -a random1.agp -ofa ``` SAK reverse complement: ``` -cat testFiles/random1.rvcp.sak +cat random1.rvcp.sak ``` ``` -gfastats testFiles/random1.fasta -ofa +gfastats random1.fasta -ofa ``` ``` -gfastats testFiles/random1.fasta -k testFiles/random1.rvcp.sak -ofa +gfastats random1.fasta -k random1.rvcp.sak -ofa ``` Other SAK instructions: ``` -cat testFiles/random1.instructions.sak -gfastats testFiles/random1.fasta -ofa -gfastats testFiles/random1.fasta -ofa -k <(head -1 testFiles/random1.instructions.sak) -gfastats testFiles/random1.fasta -ofa -k <(head -2 testFiles/random1.instructions.sak) -gfastats testFiles/random1.fasta -ofa -k <(head -3 testFiles/random1.instructions.sak) -gfastats testFiles/random1.fasta -ofa -k <(head -4 testFiles/random1.instructions.sak) -gfastats testFiles/random1.fasta -ogfa2 -k <(head -4 testFiles/random1.instructions.sak) -gfastats testFiles/random1.fasta -ofa -k <(head -5 testFiles/random1.instructions.sak) -gfastats testFiles/random1.fasta -ogfa2 -k <(head -5 testFiles/random1.instructions.sak) -gfastats testFiles/random1.fasta -ofa -k <(head -6 testFiles/random1.instructions.sak) -gfastats testFiles/random1.fasta -ogfa2 -k <(head -6 testFiles/random1.instructions.sak) -gfastats testFiles/random1.fasta -ogfa2 -k <(head -6 testFiles/random1.instructions.sak) -gfastats testFiles/random1.fasta -ogfa2 -k <(head -7 testFiles/random1.instructions.sak) -gfastats testFiles/random1.fasta -ofa -k <(head -8 testFiles/random1.instructions.sak) +cat random1.instructions.sak +gfastats random1.fasta -ofa +gfastats random1.fasta -ofa -k <(head -1 random1.instructions.sak) +gfastats random1.fasta -ofa -k <(head -2 random1.instructions.sak) +gfastats random1.fasta -ofa -k <(head -3 random1.instructions.sak) +gfastats random1.fasta -ofa -k <(head -4 random1.instructions.sak) +gfastats random1.fasta -ogfa2 -k <(head -4 random1.instructions.sak) +gfastats random1.fasta -ofa -k <(head -5 random1.instructions.sak) +gfastats random1.fasta -ogfa2 -k <(head -5 random1.instructions.sak) +gfastats random1.fasta -ofa -k <(head -6 random1.instructions.sak) +gfastats random1.fasta -ogfa2 -k <(head -6 random1.instructions.sak) +gfastats random1.fasta -ogfa2 -k <(head -6 random1.instructions.sak) +gfastats random1.fasta -ogfa2 -k <(head -7 random1.instructions.sak) +gfastats random1.fasta -ofa -k <(head -8 random1.instructions.sak) ``` diff --git a/docs/kreeq.md b/docs/kreeq.md index d9ba647..4eb0f04 100644 --- a/docs/kreeq.md +++ b/docs/kreeq.md @@ -1,3 +1,7 @@ +Let's get some test files first: +``` +mv testFiles-kreeq/* . +``` ``` kreeq validate -f input.[fasta|fastq][.gz] -r reads1.fastq[.gz] reads2.fastq[.gz] [...] [-k 21] ``` @@ -7,22 +11,22 @@ It accepts multiple read files as input, separated by space. To check out all op You can test some typical usage with the files in the `testFiles` folder, e.g.: ``` -kreeq validate -f testFiles/random1.fasta -r testFiles/random1.fastq +kreeq validate -f random1.fasta -r random1.fastq ``` Importantly, the kreeq database can only be computed once on the read set, and reused for multiple analyses to save runtime: ``` -kreeq validate -r testFiles/random1.fastq -o db.kreeq -kreeq validate -f testFiles/random1.fasta -d db.kreeq +kreeq validate -r random1.fastq -o db.kreeq +kreeq validate -f random1.fasta -d db.kreeq ``` Similarly, kreeq databases can be generated separately for multiple inputs and combined, with increased performance in HPC environments: ``` -kreeq validate -r testFiles/random1.fastq -o random1.kreeq -kreeq validate -r testFiles/random2.fastq -o random2.kreeq +kreeq validate -r random1.fastq -o random1.kreeq +kreeq validate -r random2.fastq -o random2.kreeq kreeq union -d random1.kreeq random2.kreeq -o union.kreeq -kreeq validate -f testFiles/random1.fasta -d union.kreeq +kreeq validate -f random1.fasta -d union.kreeq ``` diff --git a/docs/testFiles/random1.agp b/docs/testFiles-gfastats/random1.agp similarity index 100% rename from docs/testFiles/random1.agp rename to docs/testFiles-gfastats/random1.agp diff --git a/docs/testFiles/random1.fasta b/docs/testFiles-gfastats/random1.fasta similarity index 100% rename from docs/testFiles/random1.fasta rename to docs/testFiles-gfastats/random1.fasta diff --git a/docs/testFiles/random1.fasta.bed b/docs/testFiles-gfastats/random1.fasta.bed similarity index 100% rename from docs/testFiles/random1.fasta.bed rename to docs/testFiles-gfastats/random1.fasta.bed diff --git a/docs/testFiles/random1.gfa2 b/docs/testFiles-gfastats/random1.gfa2 similarity index 100% rename from docs/testFiles/random1.gfa2 rename to docs/testFiles-gfastats/random1.gfa2 diff --git a/docs/testFiles/random1.instructions.sak b/docs/testFiles-gfastats/random1.instructions.sak similarity index 100% rename from docs/testFiles/random1.instructions.sak rename to docs/testFiles-gfastats/random1.instructions.sak diff --git a/docs/testFiles/random1.rvcp.sak b/docs/testFiles-gfastats/random1.rvcp.sak similarity index 100% rename from docs/testFiles/random1.rvcp.sak rename to docs/testFiles-gfastats/random1.rvcp.sak diff --git a/docs/testFiles/random2.gfa b/docs/testFiles-gfastats/random2.gfa similarity index 100% rename from docs/testFiles/random2.gfa rename to docs/testFiles-gfastats/random2.gfa diff --git a/docs/testFiles/random2.noseq.gfa b/docs/testFiles-gfastats/random2.noseq.gfa similarity index 100% rename from docs/testFiles/random2.noseq.gfa rename to docs/testFiles-gfastats/random2.noseq.gfa diff --git a/docs/testFiles/random5.findovl.gfa b/docs/testFiles-gfastats/random5.findovl.gfa similarity index 100% rename from docs/testFiles/random5.findovl.gfa rename to docs/testFiles-gfastats/random5.findovl.gfa diff --git a/docs/testFiles-kreeq/random1.fasta b/docs/testFiles-kreeq/random1.fasta new file mode 100644 index 0000000..a19c3c7 --- /dev/null +++ b/docs/testFiles-kreeq/random1.fasta @@ -0,0 +1,18 @@ +>sequence1 - no errors +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAATGATAGCATGACTCAGACTGATCAGATCGA +>sequence2 - two point errors apart (25:T>A, 65:C>T) +CATACTACGATCAGATCGACTGACaCGTACATGCAGTGATGTACGAATGCATGCATCGATCGATtGAAATGATAGCATGACTCAGACTGATCAGATCGA +>sequence3 - one insertion error (34:A) +CATACTACGATCAGATCGACTGACTCGTACATGaCAGTGATGTACGAATGCATGCATCGATCGATCGAAATGATAGCATGACTCAGACTGATCAGATCGA +>sequence4 - one deletion error (34:C) +CATACTACGATCAGATCGACTGACTCGTACATGAGTGATGTACGAATGCATGCATCGATCGATCGAAATGATAGCATGACTCAGACTGATCAGATCGA +>sequence5 - one homopolymer insertion error (69:A) +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAaATGATAGCATGACTCAGACTGATCAGATCGA +>sequence6 - one homopolymer deletion error (68:A) +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGATCGATCGAATGATAGCATGACTCAGACTGATCAGATCGA +>sequence7 - two point errors overlapping (25:T>A, 35:C>T) +CATACTACGATCAGATCGACTGACaCGTACATGCtGTGATGTACGAATGCATGCATCGATCGATCGAAATGATAGCATGACTCAGACTGATCAGATCGA +>sequence8 - one point error masked by other region (25:T>A, 35:C>T) +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAATGcTAGCATGACTCAGACTGATCAGATCGA +>sequence9 - one point error masked by same kmers elsewhere (50:C>T) +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATGtATGCATCGATCGATCGAAATGATAGCATGACTCAGACTGATCAGATCGA diff --git a/docs/testFiles-kreeq/random1.fastq b/docs/testFiles-kreeq/random1.fastq new file mode 100644 index 0000000..0e64c0f --- /dev/null +++ b/docs/testFiles-kreeq/random1.fastq @@ -0,0 +1,48 @@ +@1:1-40 perfect read +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@2:10-50 perfect read +ATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@3:20-60 perfect read +CTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@4:30-70 perfect read +CATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@5:40-80 perfect read +TGTACGAATGCATGCATCGATCGATCGAAATGATAGCATG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@6:50-90 perfect read +CATGCATCGATCGATCGAAATGATAGCATGACTCAGACTG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@7:60-100 perfect read +TCGATCGAAATGATAGCATGACTCAGACTGATCAGATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@8:1-28 error masking read for sequence8 +TCGATCGAAATGcTAGCATGACTCAGACTGATCAGATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@9:29-52 error masking read for sequence9 (left) +tCATGCAGTGATGTACGAATGtA ++ +!!!!!!!!!!!!!!!!!!!!!!! +@10:29-52 error masking read for sequence9 (right) +ACATGCAGTGATGTACGAATGtc ++ +!!!!!!!!!!!!!!!!!!!!!!! +@11:29-52 error masking read for sequence9 (both) +tCATGCAGTGATGTACGAATGtc ++ +!!!!!!!!!!!!!!!!!!!!!!! +@12:29-52 error masking read for sequence9 (none) +ACATGCAGTGATGTACGAATGtA ++ +!!!!!!!!!!!!!!!!!!!!!!! diff --git a/docs/testFiles-kreeq/random2.fastq b/docs/testFiles-kreeq/random2.fastq new file mode 100644 index 0000000..3ba12d7 --- /dev/null +++ b/docs/testFiles-kreeq/random2.fastq @@ -0,0 +1,280 @@ +@1_1:1-40 +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@1_2:10-50 +ATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@1_3:20-60 +CTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@1_4:30-70 +CATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@1_5:40-80 +TGTACGAATGCATGCATCGATCGATCGAATGATAGCATGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@1_6:50-90 +CATGCATCGATCGATCGAATGATAGCATGACTCAGACTGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@1_7:60-100 +TCGATCGAATGATAGCATGACTCAGACTGATCAGATCGAC ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@2_1:1-40 +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@2_2:10-50 +ATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@2_3:20-60 +CTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@2_4:30-70 +CATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@2_5:40-80 +TGTACGAATGCATGCATCGATCGATCGAATGATAGCATGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@2_6:50-90 +CATGCATCGATCGATCGAATGATAGCATGACTCAGACTGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@2_7:60-100 +TCGATCGAATGATAGCATGACTCAGACTGATCAGATCGAC ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@3_1:1-40 +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@3_2:10-50 +ATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@3_3:20-60 +CTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@3_4:30-70 +CATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@3_5:40-80 +TGTACGAATGCATGCATCGATCGATCGAATGATAGCATGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@3_6:50-90 +CATGCATCGATCGATCGAATGATAGCATGACTCAGACTGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@3_7:60-100 +TCGATCGAATGATAGCATGACTCAGACTGATCAGATCGAC ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@4_1:1-40 +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@4_2:10-50 +ATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@4_3:20-60 +CTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@4_4:30-70 +CATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@4_5:40-80 +TGTACGAATGCATGCATCGATCGATCGAATGATAGCATGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@4_6:50-90 +CATGCATCGATCGATCGAATGATAGCATGACTCAGACTGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@4_7:60-100 +TCGATCGAATGATAGCATGACTCAGACTGATCAGATCGAC ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@5_1:1-40 +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@5_2:10-50 +ATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@5_3:20-60 +CTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@5_4:30-70 +CATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@5_5:40-80 +TGTACGAATGCATGCATCGATCGATCGAATGATAGCATGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@5_6:50-90 +CATGCATCGATCGATCGAATGATAGCATGACTCAGACTGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@5_7:60-100 +TCGATCGAATGATAGCATGACTCAGACTGATCAGATCGAC ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@6_1:1-40 +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@6_2:10-50 +ATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@6_3:20-60 +CTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@6_4:30-70 +CATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@6_5:40-80 +TGTACGAATGCATGCATCGATCGATCGAATGATAGCATGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@6_6:50-90 +CATGCATCGATCGATCGAATGATAGCATGACTCAGACTGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@6_7:60-100 +TCGATCGAATGATAGCATGACTCAGACTGATCAGATCGAC ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@7_1:1-40 +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@7_2:10-50 +ATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@7_3:20-60 +CTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@7_4:30-70 +CATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@7_5:40-80 +TGTACGAATGCATGCATCGATCGATCGAATGATAGCATGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@7_6:50-90 +CATGCATCGATCGATCGAATGATAGCATGACTCAGACTGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@7_7:60-100 +TCGATCGAATGATAGCATGACTCAGACTGATCAGATCGAC ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@8_1:1-40 +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@8_2:10-50 +ATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@8_3:20-60 +CTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@8_4:30-70 +CATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@8_5:40-80 +TGTACGAATGCATGCATCGATCGATCGAATGATAGCATGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@8_6:50-90 +CATGCATCGATCGATCGAATGATAGCATGACTCAGACTGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@8_7:60-100 +TCGATCGAATGATAGCATGACTCAGACTGATCAGATCGAC ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@9_1:1-40 +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@9_2:10-50 +ATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@9_3:20-60 +CTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@9_4:30-70 +CATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@9_5:40-80 +TGTACGAATGCATGCATCGATCGATCGAATGATAGCATGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@9_6:50-90 +CATGCATCGATCGATCGAATGATAGCATGACTCAGACTGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@9_7:60-100 +TCGATCGAATGATAGCATGACTCAGACTGATCAGATCGAC ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@10_1:1-40 +CATACTACGATCAGATCGACTGACTCGTACATGCAGTGAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@10_2:10-50 +ATCAGATCGACTGACTCGTACATGCAGTGATGTACGAATG ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@10_3:20-60 +CTGACTCGTACATGCAGTGATGTACGAATGCATGCATCGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@10_4:30-70 +CATGCAGTGATGTACGAATGCATGCATCGATCGATCGAAT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@10_5:40-80 +TGTACGAATGCATGCATCGATCGATCGAATGATAGCATGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@10_6:50-90 +CATGCATCGATCGATCGAATGATAGCATGACTCAGACTGA ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@10_7:60-100 +TCGATCGAATGATAGCATGACTCAGACTGATCAGATCGAC ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!