Description Usage Arguments Details Value Examples
Fermikit is a de novo assembly based variant calling pipeline for Illumina short reads
1 2 3 | run_bwamem(fq, kitpath = "/home/jolyang/bin/fermikit", s = "3g",
t = 16, l = 100, arrayjobs = "1-2", jobid = "fermi",
email = NULL)
|
fq |
An input data.frame for fastq files. Must contains fq1, fq2 and out. |
kitpath |
The absolute or relative path of the fermi.kit directory that can invoke the pipeline. |
s |
Approximate genome size, default=3g. |
t |
Number of threads, default=16. |
l |
Primary read length, default=100. |
arrayjobs |
A character specify the number of array you try to run, i.e. 1-100. |
jobid |
The job name show up in your sq NAME column. |
email |
Your email address that farm will email to once the job was done/failed. |
genome |
The full path of genome with bwa indexed reference fasta file. |
see more detail about fermikit by Li, Heng: https://github.com/lh3/fermikit
return a batch of shell scripts.
1 2 3 4 |
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