Add viralrecon example

Author: vladsavelyev

public/examples/viralrecon/assembly/cutadapt/fastqc/SAMPLE1_PE.primer_trim_1_fastqc.html

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public/examples/viralrecon/assembly/cutadapt/fastqc/SAMPLE1_PE.primer_trim_1_fastqc.zip

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+S1	E1	S2	E2	Reference	Contig	IDY	Ambiguous	Best_group
+8889	29839	20973	23	MN908947.3	NODE_1_length_20973_cov_191.628850	99.98		True
+CONTIG	NODE_1_length_20973_cov_191.628850	20973	correct
+32	8680	6	8654	MN908947.3	NODE_2_length_8774_cov_178.828033	99.98		True
+CONTIG	NODE_2_length_8774_cov_178.828033	8774	correct
+CONTIG	NODE_3_length_5513_cov_3.252506	5513	unaligned

public/examples/viralrecon/assembly/cutadapt/fastqc/SAMPLE1_PE.primer_trim_2_fastqc.html

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+S1	E1	S2	E2	Reference	Contig	IDY	Ambiguous	Best_group
+8889	19296	10408	1	MN908947.3	NODE_1_length_10409_cov_158.939603	99.98		True
+CONTIG	NODE_1_length_10409_cov_158.939603	10409	correct
+19317	23814	1	4498	MN908947.3	NODE_2_length_4514_cov_119.386825	99.93		True
+CONTIG	NODE_2_length_4514_cov_119.386825	4514	correct
+4569	8661	4093	1	MN908947.3	NODE_3_length_4093_cov_154.769793	99.98		True
+CONTIG	NODE_3_length_4093_cov_154.769793	4093	correct
+CONTIG	NODE_4_length_4070_cov_3.078367	4070	unaligned
+25674	29703	1	4029	MN908947.3	NODE_5_length_4051_cov_180.829511	99.85		True
+CONTIG	NODE_5_length_4051_cov_180.829511	4051	correct
+31	3853	1	3823	MN908947.3	NODE_6_length_3823_cov_156.675866	100.0		True
+CONTIG	NODE_6_length_3823_cov_156.675866	3823	correct
+23760	25672	1913	1	MN908947.3	NODE_7_length_1913_cov_76.844345	100.0		True
+CONTIG	NODE_7_length_1913_cov_76.844345	1913	correct
+CONTIG	NODE_8_length_845_cov_2.342618	845	unaligned
+CONTIG	NODE_9_length_517_cov_0.835897	517	unaligned

public/examples/viralrecon/assembly/cutadapt/fastqc/SAMPLE1_PE.primer_trim_2_fastqc.zip

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+S1	E1	S2	E2	Reference	Contig	IDY	Ambiguous	Best_group
+12936	29834	1	16899	MN908947.3	NODE_1_length_16925_cov_169.993511	99.99		True
+CONTIG	NODE_1_length_16925_cov_169.993511	16925	correct
+31	8680	1	8650	MN908947.3	NODE_2_length_8770_cov_159.215434	99.99		True
+CONTIG	NODE_2_length_8770_cov_159.215434	8770	correct
+CONTIG	NODE_3_length_5513_cov_3.337542	5513	unaligned
+8889	13062	1	4174	MN908947.3	NODE_4_length_4174_cov_117.278972	99.98		True
+CONTIG	NODE_4_length_4174_cov_117.278972	4174	correct

public/examples/viralrecon/assembly/cutadapt/fastqc/SAMPLE2_PE.primer_trim_1_fastqc.html

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+[M::mm_idx_gen::0.058*0.75] collected minimizers
+[M::mm_idx_gen::0.071*0.72] sorted minimizers
+[M::main::0.085*0.60] loaded/built the index for 1 target sequence(s)
+[M::mm_mapopt_update::0.091*0.57] mid_occ = 200
+[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1
+[M::mm_idx_stat::0.099*0.54] distinct minimizers: 3006 (100.00% are singletons); average occurrences: 1.000; average spacing: 9.948; total length: 29903
+[M::worker_pipeline::0.664*0.42] mapped 3 sequences
+[M::main] Version: 2.24-r1122
+[M::main] CMD: /usr/local/bin/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 /Users/vlad/git/viralrecon/work/90/8841f5f3c5cd6598a8d31a58bb0c66/quast/quast_corrected_input/nCoV-2019.reference.fasta /Users/vlad/git/viralrecon/work/90/8841f5f3c5cd6598a8d31a58bb0c66/quast/quast_corrected_input/SAMPLE1_PE-scaffolds.fa
+[M::main] Real time: 0.677 sec; CPU: 0.286 sec; Peak RSS: 0.146 GB