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Comment on "Short-read assembly using Spades !"
...ommand for running SPAdes is usually as follows: spades.py -o output_directory -1 forward_reads.fastq -2 reverse_reads.fastq Here, "output_directory" is the name of the directory...430 days ago
Comment on "How to install Perl modules manually, using CPAN command, and other quick ways"
...bsp;perl - it should give you the perl that's located within your conda environment. In this case, it should install things into your conda-directory. When you install packages v...431 days ago
Comment on "Short-read assembly using Spades !"
...Run SPAdes: To run SPAdes, open the terminal and navigate to the directory where the input data is store...paired-end reads, and <output_dir> with the name of the output directory where the assembled contigs w...436 days ago
- ...mes: $ ./fastANI -q [QUERY_GENOME] --rl [REFERENCE_LIST] -o [OUTPUT_FILE] For above use case, REFERENCE_LIST should be a file containing directory paths to reference genomes, o...
1116 days ago
Comment on "Sibelia: A comparative genomics tool"
...with "Sibelia" executable. Directory "examples/Sibelia" contains t...mporary files, try to change directory used for temporary files (see...ters ==================== Directory for output files -----------...such diagram are written in directory "circos" inside the output di...1300 days ago
Comment on "Mugsy: multiple whole genome alignment tool"
...Run mugsy mugsy --directory /data/output --prefix mygenom...ign three genomes and output a file /data/output/mygenomes.maf. The --directory setting is also used for stor...1300 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
...e sure that you use the flags for canonical hashes for both sequence 1 and 2, as well as 8 threads. Finally, clean up you working directory by removing the combined fast...1352 days ago
- ...ecifications-file>] \ -p <assembly-prefix> \ -d <assembly-directory> \ genomeSize=<number&g...d then assemble them The assembly is computed in the -d <assembly-directory>, with output files named...
2114 days ago
- ...y-prefix> \ -d <assembly-directory> \ genomeSiz...is computed in the (created) -d <assembly-directory>, with most files named...enome.2D.10.fasta This puts output in directory meta with prefix “meta&...
2190 days ago
- ...ads (<= 100, default 1) -o STR : Prefix of output files (default out, length <= 200) -tmp DIR : directory for temporary files (default . (working directory)) ------------------------...
2814 days ago
