Results for "fast mapping"
Bio-Scripts
#!/usr/local/bin/perl -w # NOTE: YOU MUST CHANGE THE LINE ABOVE TO POINT TO # THE FU...second sequence with option -j. is a fasta format file from which the...is is the only required parameter. is a fasta f...2704 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## uses pod documentation in usage code use Getopt::Long qw(:config auto_version auto_he...2320 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any re...-mem or BWA-sampe in one go. An example call for mapping with this scr...to/lib1_A.fq /path/to/lib1_B.fq /path/to/contigs.fasta --threads N where N is an inte...2135 days ago
Install Parrot Virtual Machine !
#Parrot is a virtual machine designed to efficiently compile and execute bytecode for dynamic languages jit@ji...d -X --dynext add path to dynamic extension search -R --runcore fast|sl...1548 days ago
Long reads mapper bash script !
...ho "Name of the file used for mapping $fileName, present at $refFas...me == "bwa" ]; then echo "Mapping with $toolName" $bwaMemLo...aln -t $thread -T pacbio $refFasta $longReads > $fileName.out.sam...== "ngmlr" ]; then echo "Mapping with $toolName" if [ $reads...2134 days ago
- ...(if --assembly is given) 2. read mapping based (if --left and --rig...ly= Assembly file(s) in FASTA format, comma-separated -...Left reads file(s) in FASTQ format, comma-separated -...86_64/transrate --assembly=Trinity.fasta --output=transrateSTAT [ INFO]...
2134 days ago
- ➜ upgrade_oh_my_zsh Updating Oh My Zsh remote: Counting objects: 484,.../master Updating 9544316e..dc8811f8 Fast-forward lib/functions.zsh...| 4 +- plugins/mix-fast/README.md...| 2 +- plugins/rake-fast/RE...
2086 days ago
- bwa aln -t 8 targetGenome.fa reads.fastq | bwa samse targetGenome.fa - reads.fastq\ | samtools view -bt targetGenome.fa - | samtools sort - reads.bwa.targetGenome samtools index reads.bwa.targetGenome.bam
1845 days ago
Bash script to alignment of short reads against reference genome !
...coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.fastq.gz \ | samtools view -b...ample name K12" #reference and FASTQs E.coli_K12_MG1655.fa SRR177...duplicates based on their read mapping position. It uses the same....coli_K12_MG1655.fa SRR341549_1.fastq.gz SRR341549_2.fastq.gz \...1570 days ago
Installing docker for Bioinformatics on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove docker docker-engine d...ause all processes within one or more containers port List port mappings or a specific mapping for the container ps...1524 days ago
