Results for "de novo assembly"
Bio-Scripts
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"}...2530 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"}...2521 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## u...ry"}){ pod2usage({-exitVal => 1, -message => "Error: No query assembly file provided",...2306 days ago
- ...DESCRIPTION: Analyse a de-novo transcriptome assembly using three kinds of metrics: 1. sequence based (if --assembly is given) 2. read mapping ba...explanations ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1....a/urbe/MyPassport/BorisTrinityAssembly/transrateSTAT/Trinity/contigs...
2121 days ago
Resume the MIRA assembler run !
mira -r manifest_file Usage: mira [options] manifest_file [manifest_file ...]...orking directory -r / --resume Resume an interupted assembly -h / --help...1732 days ago
- set -e echo "Running reapr version 1.0.1...ls/Reapr_1.0.18/reapr score -P 5 00.assembly.fa.gaps.gz 00.in.bam 01.stats...e/Tools/Reapr_1.0.18/reapr break 00.assembly.fa 03.score.errors.gff.gz 04....ls/Reapr_1.0.18/reapr score -P 5 00.assembly.fa.gaps.gz 00.in.bam 01.stats...
2097 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://gith...Call germline SNPs and indels via local re-assembly of haplotypes HaplotypeC...Call somatic SNVs and indels via local assembly of haplotypes ReadsPipel...
2073 days ago
Installing pb-assembly on Linux !
...@hmem00 ~]$ conda create -n denovo_asm [jnarayan@hmem00 ~]$ source activate denovo_asm (denovo_asm) [jnarayan...h470a237_0 conda-forge pb-assembly 0.0.1...70a237_3 conda-forge (denovo_asm) [jnarayan@hmem00 ~]$ fc fc...2032 days ago
- (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git...' already exists and is not an empty directory. (denovo_asm) [jnarayan@hmem00 ~]$ git...done. Resolving deltas: 100% (398/398), done. (denovo_asm...
2032 days ago
Setting up falconUnzip conda environments for genome assembly !
...: /home/urbe/anaconda3/envs/denovo_asm added / updated specs: - pb-assembly The following packages w...conda-forge pb-assembly: 0.0.2-py27_0...################# | 100% pb-assembly-0.0.2 | 4 KB | ######...1988 days ago
