Results for "bwa"
Bio-Scripts
Mapping with BWA-mem or BWA-sampe in one go with python script !
...T provides a script (https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obtaining sorted and indexed BAM files with BWA-mem or BWA-sampe in one go. An example c...2130 days ago
Long reads mapper bash script !
...minimap2Loc=/home/urbe/Tools/minimap2-2.3_x64-linux/minimap2 bwaMemLoc=/home/urbe/anaconda3/bin/bwa ngmlrLoc=/home/urbe/Tools/ng...mapping $fileName, present at $refFasta" if [ $toolName == "bwa" ]; then echo "Mapping wi...2129 days ago
- ...Builds a taxonomy datafile of the microbe reference PathSeqBwaSpark...(Picard) Generates a BAM index ".bai" file. BwaAndMarkDuplicatesPipelineSpark...
2081 days ago
Installing pb-assembly on Linux !
...dd channels conda-forge (denovo_asm) [jnarayan@hmem00 ~]$ conda install bwa Fetching package metadata .....envs/denovo_asm: The following NEW packages will be INSTALLED: bwa: 0.7.17-ha92aebf_3 bioc...2040 days ago
Setting up falconUnzip conda environments for genome assembly !
...blasr: 5.3.2-hac9d22c_3 bioconda blasr_libcpp: 5.3.1-hac9d22c_2 bioconda bwa: 0.7.17-h...1996 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
1840 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
1732 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \...ng it down by line: #alignment with bwa: bwa mem -t $threads -R '@RG\...pecifies the base reference file name (bwa finds the indexes using this)...ap2.bam #The only major change from bwa mem is that we'll tell it we'...1565 days ago
Bash command to install bwa, samtools, picard !
...su29@bladeamd-2 tmp]$ conda install bwa Collecting package metadata...added / updated specs: - bwa The following packages w...py37_1 3 KB bwa-0.7.17 |..._anaconda_depends-2019.03-py37_0 bwa bioconda/linux...1562 days ago
Pack a perl program with their dependencies on Ubuntu !
...genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li.......1517 days ago
