Results for "B"
Bio-Scripts
Resume the MIRA assembler run !
.....] Options: -c / --cwd= directory Change working directory -r / --resume Resume an interupted assembly -h / --help...1788 days ago
- # Convert FASTQ to FASTA seqtk seq -a IN.fastq > OUT.fasta # Convert FASTQ to FASTA and set bases of quality lower than 20 to N seqtk seq -aQ64 -q20 -n N IN.fastq > OUT.fasta # Download Seqtk https://github.com/lh3/seqtk
1779 days ago
- Map them agaist reference avaga genome using following codes git clone https://github.com/lh3/bwa.git cd bwa; make bwa index ref.fa bwa mem -x pacbio ref.fa pacbio.fq > aln.sam bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam
1778 days ago
- #!/bin/bash cd `pwd` perl ~/apps/SSPACE-1.2_linux-x86_64/SSPACE_v1-2.pl \ -l libraries.txt \ -s Contigs_over200_nocp.fasta \ -k 5 \ -a 0.7 \ -x 1 \ -m 30 \ -o 20 \ -b Rayk31_scaffolds_extension
1776 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use war...se Parallel::ForkManager; use Bio::SeqIO; my ($sequence_da...$pm->wait_all_children; sub output_exists { my $chr_...rameters $chr_set!\n"; } sub touch { my ($fn, $seq) =...$sequence_data{$accession_number}{status} = "OK"; #everybody...1740 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 script1669 days ago
- ...module load samtools NUM_BP=`samtools depth $2 | perl -e...}} print "$c\n";'` echo "num bp: "$NUM_BP NUM_SNP=`cat $1...\t"$8}' | tr ';' ' ' | sed s/AB=//g | awk -v WEIGHT=0 '{if ($...GV[1]; print (-10 * log($ns/$nb)/log(10)); print "\n";' $NUM_...
1658 days ago
Samtools commands for bioinformatician !
...put file name samtools view -b -S -o sal_sej.bam sal_sej.sam...atches samtools -F 4 sal_sej.bam | less ### count reads..._ref_sej.fasta sal_sej_sorted.bam.bam > sal_vars.bcf ###...ls depth -a sorted_dupremoved.bam | awk '{c++;s+=$3}END{print...1656 days ago
Perl subroutine to creating kmer !
sub k_mers { my ($sequence, $k) = @_; my $len = length($sequence); my @result = (); for (my $i = 0; $i1620 days ago
Perl script to remove duplicated lines !
#!/usr/bin/perl use strict; use warnings; { $_ = ; my $next_line; wh...e; } print $_ if eof; } __DATA__ apple apple plum vinegar apple banana banana banana apple1613 days ago
