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denovo2013 [2017/11/01 04:50]
telatina
denovo2013 [2017/11/13 03:01] (current)
telatina
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 ==== 1.3. Assembly ==== ==== 1.3. Assembly ====
 === The Velvet assembler === === The Velvet assembler ===
-[[https://​www.ebi.ac.uk/​~zerbino/​velvet/​|Velvet]] has been on of the first reliable implementation of the De Bruijn ([[http://​www.cs.jhu.edu/​~langmea/​resources/​lecture_notes/​assembly_dbg.pdf|slides]]) graphs for short reads //de novo// assembly. It has not been updated in the last years, but it's worth trying, because of its simple workflow. It consists of two programs: ''​velveth'' ​calculates ​the graph, while ''​velvetg'' ​explores it to extract contigs. The "​Output directory"​ of ''​velveth''​ is thus the //input// directory of ''​velvetg''​.+[[https://​www.ebi.ac.uk/​~zerbino/​velvet/​|Velvet]] has been on of the first reliable implementation of the De Bruijn ([[http://​www.cs.jhu.edu/​~langmea/​resources/​lecture_notes/​assembly_dbg.pdf|slides]]) graphs for short reads //de novo// assembly. It has not been updated in the last years, but it's worth trying, because of its simple workflow. It consists of two programs: ''​velveth'' ​counts all the //k//-mer occurrences, while ''​velvetg'' ​does the actual assembly. The "​Output directory"​ of ''​velveth''​ is thus the //input// directory of ''​velvetg''​.
 <code bash> <code bash>
 # Example using 47 as k-mer size # Example using 47 as k-mer size
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 velvetg OutputDirectoryName -clean yes -exp_cov auto -cov_cutoff auto -min_contig_lgth 180 velvetg OutputDirectoryName -clean yes -exp_cov auto -cov_cutoff auto -min_contig_lgth 180
 </​code>​ </​code>​
 +
 +lesskl
 === The Spades assembler === === The Spades assembler ===
-velveth out_data_35 35 -fastq.gz -shortPaired -separate SRR292770_1.fastq.gz SRR292770_2.fastq.gz+
  
 ===== 2. Comparative Genome analysis ===== ===== 2. Comparative Genome analysis =====