Results for "N50"
Bio-Scripts
...### ### Script Name : calcN50.pl ### Description : This script calculates the N50 of a collection of sequences...quence to consider it for the N50 calculation ### Output...v (@sorted) { if($v >= $N50) { $count++; } }...2697 days ago
- ...13 14:54:34 : n90 748 [ INFO] 2018-07-13 14:54:34 : n70 1578 [ INFO] 2018-07-13 14:54:34 : n50 22...
2116 days ago
- ...stq.gz in2=illumina2.fastq.gz out=illumina.int.fastq 2>/dev/null # use KmerGenie 1.7051 to get an idea of k-mer with that produces longest N50 # http://kmergenie.bx.psu.ed...
921 days ago
Bash script to simulate a genome !
...stq.gz in2=illumina2.fastq.gz out=illumina.int.fastq 2>/dev/null # use KmerGenie 1.7051 to get an idea of k-mer with that produces longest N50 # http://kmergenie.bx.psu.ed...911 days ago
Extract fasta header with ids !
...out.fa more out.fa_class.txt | grep "227859" | awk '{print $2}' > all_real_ids.txt minimap2 -t 36 -k19 -w5 -A1 -B2 -O3,13 -E2,1 -s200 -z200 -N50 --min-occ-floor=100 finaal_ou...870 days ago
Perl script to calculate the basic stats of the assembled genome !
...ngths[0]; my $avg_contig_length = $total_length / $num_contigs; my $median_contig_length = calculate_median(\@contig_lengths); # Calculate N50 my $n50 = calculate_n50(\@contig_leng...87 days ago
Python script for basic stats of the assembled genome !
...an_contig_length = statistics.median(contig_lengths) # Calculate N50 def calculate_n50(lengths): total_size = s...") print(f"Median Contig Length: {median_contig_length}") print(f"N50: {calculate_n50(contig_length...87 days ago
