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Mangul-Lab-USC / needle

Needle (full name: Needle in a haystack) combines alignment and assembly for comprehensive virome, mycobiome, and eukaryome profiling on the strain level.
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edit distance #3

Open smangul1 opened 5 years ago

smangul1 commented 5 years ago

hisat2.tuned_26-002-D4_S85_R1_001.fastq_unmapped.fastq.protozoa.megahit.contigs.SV.filtered.csv

k61_11,NC_007268.2,Leishmania_major_strain_Friedlin_complete_genome__chromosome_27,153,58,206,-163.793103448,no-blast

k61_11 16 NC_025260.1 904367 0 64S103M39S 0 0 TTACTAAGAAATACACCAAGCAAAAGCAAGGCTGAGTCCCAGCAACGCGACTGACTTCAAGCGTTTCCCTTTCAACAATTTCACGTACTGTTAACTCTCTTTCCAAAGTGCTTTTCATCTTTCCCTCACGGTACTTGTTTGCTATCGGTCTCTCGCCAATATTTAGCTTTAGATGGAATTTACCACCCAATTTGAGCTGCATTCCC NM:i:13 MD:Z:10G2G5G5T5A2T3T6A26C1A0C12A1A12 AS:i:38 XS:i:38

smangul1 commented 5 years ago

contig, id, name, number_mismatches=153 alignment_length, contig_length, adjusted_identity,flag

smangul1 commented 5 years ago

5 206 58 148 number_mismatches, 5 read_length, 55+33+25+93=206 alignment_length=58 soft=148

edit distance=(58-5)/206

k61_11 256 26 993308 0 55H33M1D25M93H -1 -1 58 None None [('NM', 5), ('MD', '11G8G6C5^T0T24'), ('AS', 31)]