2240 days ago
2106 days ago
Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2086 days ago
Generate simulated polyploid genome !
...t both files cat toy.fasta toymutated3percent.fasta > toyheterozygous3percent.fasta #generated 50X of Illumina paired-end reads sim_reads --depth 50 toyheterozygous3percent.fa...2084 days ago
2034 days ago
1635 days ago
Samtools commands for bioinformatician !
...sorted.bam.bam sal_ref_sej.fasta ### results into txt file samtools depth /path/to/sorted_bam.bam > /path/to/coverage_results.txt ### note: returns count of depth at each position. input shoul...1633 days ago
Tadpole is 250x faster than SPADes assembler !
...Only dump kmers with at least this depth. showstats=t Print a...to ignore kmers with depth of that value or lower. preh...ratio of 1st to 2nd-greatest path depth at low depth. branchlower=3...his means they have no kmers above depth 1 (2 for paired...1007 days ago