725 days ago
Script to rapid genome clustering based on pairwise ANI
First, create a blast+ database: makeblastdb -in -dbtype nucl -out Next, use megablast from blast+ package to perform all-vs-all blastn of sequences: blastn -que...695 days ago
Genome Scaffolding and gap filling !
scaffolding with ARCS v1.0.3 (−c3, −l,4, −a,0.9, −z500, −m50, −20 000, −e30000, −s90). https://github.com/bcgsc/arcs Next, automated gap filling was performed using Sealer v2.0.1 (−L150, -P10, −k75-115 [step = 10]) https://github.com/bcgsc/abyss/tree/sealer-release680 days ago
Extract the mapped and unmapped reads !
...ols view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam samtools view --threads $PROCESSORS -b -f 4 in.bam > unmapped.bam #Paired_End_Layout...s view --threads $PROCESSORS -b -F 2 in.bam > unmapped.bam650 days ago
Identify genome-wide synteny with LASTZ alignment
...nment using LASTZ and Chain/Net lastz AAChr1.txt FFChr1.txt K=2200 L=6000 Y=3400 E=30 H=0 O=400 T=1 --format=axt --out=chr01.axt axtChain -linearGap=medium chr01.axt AAChr1.txt F...577 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data478 days ago
52 days ago
359 days ago
Python script to find repeats in the DNA sequence !
...substring = sequence[i:i+min_repeat_length] if sequence.count(substring) > 1 and substring not in repeats: repeats.append(substring) ret...154 days ago
Raku script to find overlaps between two bed files !
...tart1 = @fields1[1]; my $end1 = @fields1[2]; # Check for overlaps with intervals in the second...my $end2 = @fields2[2]; # Check for chromosome match and overlap if $chr1 eq $chr2 &&...154 days ago