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Cloud-SPAN / metagenomics02-polishing

Metagenomics Polishing lesson
https://cloud-span.github.io/metagenomics02-polishing
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Exercise 1: Flag to get the N50 length #9

Open 3mmaRand opened 1 year ago

3mmaRand commented 1 year ago

correct commands given in solution so paths correct

3mmaRand commented 1 year ago

also give the results for pilon/pilon.fasta and assembly/assembly.fasta

csuser@metagenomicsT3instance04:~/cs_course/analysis $ seqkit stats -a pilon/pilon.fasta
file               format  type  num_seqs     sum_len  min_len   avg_len    max_len     Q1        Q2      Q3  sum_gap        N50  Q20(%)  Q30(%)  GC(%)
pilon/pilon.fasta  FASTA   DNA        154  15,070,837    3,144  97,862.6  6,074,532  7,175  13,279.5  34,010        0  2,992,063       0       0  52.27
csuser@metagenomicsT3instance04:~/cs_course/analysis $ seqkit stats -a assembly/assembly.fasta
file                     format  type  num_seqs     sum_len  min_len   avg_len    max_len     Q1      Q2      Q3  sum_gap        N50  Q20(%)  Q30(%)  GC(%)
assembly/assembly.fasta  FASTA   DNA        154  15,044,596    3,164  97,692.2  6,068,626  7,305  13,291  34,108        0  2,976,493       0       0  52.38
csuser@metagenomicsT3instance04:~/cs_course/analysis $