Resume the MIRA assembler run !
mira -r manifest_file Usage: mira [options] manifest_file [manifest_file ...]...orking directory -r / --resume Resume an interupted assembly -h / --help...1735 days ago
2099 days ago
2075 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 treatBAMfile2055 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheterozy...2053 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail -----...m00 ~]$ conda install -c bioconda pb-assembly Fetching package metadata .....current linux-64 channels: - pb-assembly -> genomicconsensus -> python...h470a237_0 conda-forge pb-assembly 0.0.1...2034 days ago
2034 days ago
Setting up falconUnzip conda environments for genome assembly !
...d / updated specs: - pb-assembly The following packages w...18 KB conda-forge pb-assembly-0.0.2 | py...conda-forge pb-assembly: 0.0.2-py27_0...################# | 100% pb-assembly-0.0.2 | 4 KB | ######...1990 days ago
1726 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManag...my ($sequence_data_ref) = parse_genome_files($ARGV[0]); my %genome=%{$sequence_data_ref}; my...; foreach my $chr_set (keys %genome) { $count++...e FILE or die $!; } sub parse_genome_f...1687 days ago