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"}...2522 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"}...2513 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",...2299 days ago
- ...ly 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...
2113 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...1725 days ago
- set -e echo "Running reapr version 1.0.18 p...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...
2089 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github....Call germline SNPs and indels via local re-assembly of haplotypes HaplotypeC...Call somatic SNVs and indels via local assembly of haplotypes ReadsPipel...
2066 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...2025 days ago
- (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git fatal: destination path 'git-sym' already exists and is not an empty directory. (d...
2024 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 | ######...1980 days ago
