Results for "Genome Assembly"
Bio-Scripts
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...1729 days ago
- ...r_1.0.18/reapr score -P 5 00.assembly.fa.gaps.gz 00.in.bam 01.sta.../Reapr_1.0.18/reapr break 00.assembly.fa 03.score.errors.gff.gz 04.....18/Wadineta_Afasta_gapfilled_genome/perfect.perfect_cov.gz ./ 01.st...r_1.0.18/reapr score -P 5 00.assembly.fa.gaps.gz 00.in.bam 01.stats...
2094 days ago
- ...ard) Collect whole genome sequencing-related metrics....coverage and performance of whole genome sequencing (WGS) experiments....line SNPs and indels via local re-assembly of haplotypes HaplotypeC...somatic SNVs and indels via local assembly of haplotypes ReadsPipel...
2070 days ago
Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2050 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheterozy...2048 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...2029 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...
2029 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 | ######...1984 days ago
- Map them agaist reference avaga genome using following codes git clone https://github.com/lh3/bwa.git cd bwa; make bwa index ref.fa bwa mem -x pacbio ref.fa pacbio.fq > aln.sam bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam
1720 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManag...my ($sequence_data_ref) = parse_genome_files($ARGV[0]); my %genome=%{$sequence_data_ref}; my...; foreach my $chr_set (keys %genome) { $count++...e FILE or die $!; } sub parse_genome_f...1681 days ago
