Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2057 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 > toyheteroz...2055 days ago
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving environment: done ## Package Plan ## environment location: /home/urbe/anaconda3/envs/denovo_asm Pro...1991 days ago
1727 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use war...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_files { my $file=shift;...1688 days ago
Find and replace in multifasta or fasta header with perl onliner
You have a fasta file and you want to replace: "|" You are told to replace that by "_" perl -i -p -e "s/\|/_/g" genome.fasta -i = inplace editing -p = loop over lines and print each line (after processing) -e = command line script1617 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_fi...-q 42 -c sal_sej.bam ### sorting bam file by genome position samtools sort sal_s...ols index sal_sej_sorted.bam.bam ### identifying genome variants (mpileup command) #...1605 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.fastq.gz \ | samtools view -b - >SRR1770413.raw.bam sambamba...1561 days ago
Pack a perl program with their dependencies on Ubuntu !
...p; answer key is released... Evaluation of genome assembly software based on l...y BioStar 409 days ago Evaluationgenomeassemblysoftwarelongreads...ene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data....1513 days ago
Install Ragout genome assembler
$ conda install -c bioconda ragout Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/...1466 days ago