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Comment on "Benchmarking Perl Module !"
...k for 100 iterations: timethese(100, { 'MyModule' => \&benchmark_my_module, }); Analyze the results: The timethese function will output the results of the benchmark,...451 days ago
Comment on "Short-read assembly using Spades !"
...ce. The command 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...451 days ago
Comment on "Short-read assembly using Spades !"
...: spades.py -1 <read1.fastq> -2 <read2.fastq> -o <output_dir> Replace read1.fas...h the names of the input files containing the paired-end reads, and <output_dir> with the name of the...456 days ago
Comment on "Tools for Sequence translation !"
...anslation. The choice of tool depends on the specific requirements of the user, including the input format, the genetic code used, and the type of output required....456 days ago
Comment on "URMAP, an ultra-fast read mapper"
...index filename is given by the -ufi option. A filename for SAM format output is specified by -samout. Use /dev/stdout or "-" (minus sign) if you want to pipe output to another program. The -thr...1319 days ago
Comment on "Sibelia: A comparative genomics tool"
...ents, use "fine". See also section "Output description" for detailed depiction of the output format. The "far" parameters...e> By default, "Sibelia" places output files in current working dire...default this file is not written. To output this file, set cmd parameter:...1320 days ago
Comment on "Mugsy: multiple whole genome alignment tool"
... mugsy --directory /data/output --prefix mygenomes genome1.fa...This example will align three genomes and output a file /data/output/mygenomes...ilename will be used as the genome name in the output files (eg. genome1 from genom...1321 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
... 8 threads. Finally, clean up you working directory by removing the combined fasta file, and re-zipping any unzipped files. Then download the output files to you computer using&n...1372 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
...a> will tell you if everything’s ok! in this case, no output is good output, since the only output from t.... Do the same thing you did with perfectmap and create an output file called <assemble...1372 days ago
- ...as pairs, e.g. kallisto quant -i index -o output pairA_1.fastq pairA_2.fastq p...STQ files, e.g kallisto quant -i index -o output --single -l 200 -s 20 file1.f.... Please use the --plaintext mode to output plaintext abundance estimates...
1396 days ago
