Download the genome from NCBI using bash script/command
...d genome # Look for genome assembly summary and extract the URL....nih.gov/genomes/refseq/fungi/assembly_summary.txt' | awk '{FS="\t"}....gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"}...h.gov/genomes/refseq/protozoa/assembly_summary.txt' | awk '{FS="\t"}...2525 days ago
Download the gff files from NCBI using bash script/command
...nome_gff # Look for genome assembly summary and extract the URL....nih.gov/genomes/refseq/fungi/assembly_summary.txt' | awk '{FS="\t"}....gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"}...h.gov/genomes/refseq/protozoa/assembly_summary.txt' | awk '{FS="\t"}...2516 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## use...y"}){ pod2usage({-exitVal => 1, -message => "Error: No query assembly file provided",...2301 days ago
2116 days ago
Resume the MIRA assembler run !
mira -r manifest_file Usage: mira [options] manifest_file [manifest_file ...]...rking directory -r / --resume Resume an interupted assembly -h / --help...1727 days ago
2092 days ago
2068 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail ------...m00 ~]$ conda install -c bioconda pb-assembly Fetching package metadata .....current linux-64 channels: - pb-assembly -> genomicconsensus -> python...h470a237_0 conda-forge pb-assembly 0.0.1...2027 days ago
2027 days ago
Setting up falconUnzip conda environments for genome assembly !
...d / updated specs: - pb-assembly The following packages w...18 KB conda-forge pb-assembly-0.0.2 | py...conda-forge pb-assembly: 0.0.2-py27_0...################# | 100% pb-assembly-0.0.2 | 4 KB | ######...1983 days ago