Results for "de novo assembly"
Bio-Scripts
Install StringTie on ubuntu / Linux !
#StringTie is a software program to perform transcript assembly and quantification of RNAseq data. The binary distributions are available so to install we can just download this distribution and e...838 days ago
Bash command to explore assembly summary genbank !
wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt pip3 install csvkit csvcut -t -K 1 -c 'excluded_from_refseq' assembly_summary_genbank.txt \ | tail -n +2 | tr ";" "\n" \ | sed -e 's/^ //' -e 's/ $//' | grep -v '""' \ | sort | uniq -c | sort -nr783 days ago
Perl script to calculate the basic stats of the assembled genome !
#!/usr/bin/perl use strict; use w...put file containing the genome assembly in FASTA format my $input_file = 'genome_assembly.fasta'; # Create Bio::SeqI...e through each sequence in the assembly while (my $seq = $seqio->nex...and information print "Genome Assembly Statistics:\n"; print "-----...109 days ago
Python script for basic stats of the assembled genome !
from Bio import SeqIO import stati...put file containing the genome assembly in FASTA format input_file = 'genome_assembly.fasta' # Variables for com...e through each sequence in the assembly for record in SeqIO.parse(in...and information print("Genome Assembly Statistics:") print("-------...109 days ago
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