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Ancestral sequence reconstruction steps !
..."Mafft - http://mafft.cbrc.jp/alignment/software/source.html" mafft --maxiterate 1000 --reorder --thread 24 --genafpair Dataset.fasta > Dataset_Alig.fasta 2- Your dataset has...2178 days ago
LINKS scaffolder bloomfilter setting !
...✗ ./LINKS Usage: ./LINKS [v1.8.6] -f sequences to scaffold (Multi-FASTA format, required) -s file-o...ames, full path to long sequence reads or MPET pairs [see below] (Multi-FASTA/fastq format, required) -m...2150 days ago
My commonly used commands in Bioinformatics
...con makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta racon_assembly.fasta nucmer...2109 days ago
Parallel Processing with Perl !
...thisfor example:my $number_split=int($number_of_entries_in_your_dataset/$max_processors);my $split_Files=`split -l $number_split “your_file.fasta” “file_name&rdquo...2079 days ago
Short-read assembly using Spades !
...etting, “off”) -o is the output directory Results Move into the output directory and look at the contigs: infoseq contigs.fasta...824 days ago
Steps to find all the repeats in the genome !
...ad it from the RepeatMasker website[0]. Prepare the genome sequence: Make sure you have the genome sequence in a FASTA file format. Let's assume the file is named "genome.fasta". ./RepeatMasker -pa <...247 days ago