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: don...Total: 280.6 MB The following NEW packages will be INSTALLED:...d-line users, and # # possibly newer than the currently availabl...d-line users, and # # possibly newer...1992 days ago
1727 days ago
Perl script to run in parellel !
...($sequence_data_ref) = parse_genome_files($ARGV[0]); my %genome=%{$sequence_data_ref};...foreach my $chr_set (keys %genome) { $count++...r_set.out" ); } sub start_new_XFOIL_instance { my ($chr_s...LE 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 !
...-c sal_sej.bam ### sorting bam file by genome position samtools sort sa...ndex sal_sej_sorted.bam.bam ### identifying genome variants (mpileup command) #...w -c -v sal_vars.bcf > sal_vars.vcf ### note: new command is "call". type "bcftool...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 !
...st password ActivityNewsOpportunityResearchLabsQuesti...released... Evaluation of genome assembly software based on...s ago Evaluationgenomeassemblysoftwarelongreads...and animal genomes, enabling new insights into evolution and sequ...1513 days ago
Install Ragout genome assembler
$ conda install -c bioconda ragout Collecting package metadata (repodata.json): done Solving environment: done...Total: 27.6 MB The following NEW pa...1466 days ago