Results for "FASTA"
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...eader and sequence needed for fasta format. sed -n '1~4s/^@/>...tr -s "/t" "/n" > OUTFILE.fasta EMBOSS:seqret Standard sc...h the huge datasets fastq_to_fasta -h usage: fastq_to_fasta [-h...eq -a input.fastq > output.fasta Note that you can use eith...2299 days ago
- ...}END{print seqlen}' \filename.fasta To copy (move, rename, etc)...To count all sequences in a fasta file: grep "^>" yourfile....'\n' | wc -c To split multifasta file into many fasta files:...ength($0); print }' scaffolds.fasta > 200bp_scaffolds.fasta &...
2211 days ago
- ...ibc-bin (2.23-0ubuntu10) ...➜ redundans git:(master) ✗ python2 redundans.py -v -i test/*_?.fq.gz -f test/contigs.fa -o test/run1Options: Namespace(fasta='test/contigs.fa', fastq=['te...
2184 days ago
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...2172 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...2144 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...2104 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...2073 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...818 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 <...242 days ago
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