Process the sequence after the genome and reads are aligned.
wget -c https://github.com/zxgsy520/sam2ngs/archive/v1.1.0.tar.gz
tar -zxvf v1.1.0.tar.gz
cd sam2ngs-1.1.0
chmod 755 *
or
git clone https://github.com/zxgsy520/sam2ngs.git
cd sam2ngs
chmod 755 *
sam2ngs: Extract the sequence on the genome and the second-generation data alignment (sam).
usage: sam2ngs [-h] [-i FILE] -g FILE [-d STR] [-p STR]
name:
sam2ngs Select no reads on the map
attention:
sam2ngs -i input.sam -g genome.fa -p name
minimap2 -t 8 -ax sr genome.fa r1.fq r2.fq|samblaster -a |sam2ngs -g genome.fa -p name
version: 1.1.0
contact: Xingguo Zhang <113178210@qq.com>
optional arguments:
-h, --help show this help message and exit
-i FILE, --input FILE
Input files in sam.
-g FILE, --genome FILE
Inport genome files.
-d STR, --depth STR Set the reads depth selected by each contig(Select all=all), default=200
-p STR, --prefix STR Inport the file prefix.
filter_paf：Filter low-quality comparison data (paf) of genome and reads.
usage: filter_paf [-h] [-i FILE] [-id FLOAT] [-mq INT]
name:
filter_paf.py Filter the reads comparison result file
attention:
filter_paf.py -i file.paf >file_clean.paf
cat file.paf | filter_paf.py >file_clean.paf
version: 1.1.0
contact: Xingguo Zhang <113178210@qq.com>
optional arguments:
-h, --help show this help message and exit
-i FILE, --input FILE
Input files in paf
-id FLOAT, --identities FLOAT
Set the minimum identities of reads comparison, default=50.0
-mq INT, --mapq INT Set the minimum quality value for reads alignment, default=2
sam2unmap：Extract the unaligned sequence of the genome and reads．
usage: sam2unmap [-h] [-i FILE] [-mq INT]
name:
sam2unmap Recover unmap sequence
attention:
sam2unmap -i input.sam >unmap.fastq
minimap2 -t 8 -ax sr genome.fa r1.fq r2.fq|sam2unmap >unmap.fastq
version: 1.1.0
contact: Xingguo Zhang <113178210@qq.com>
optional arguments:
-h, --help show this help message and exit
-i FILE, --input FILE
Input files in sam.
-mq INT, --minmapq INT
Set the minimum quality value for reads alignment, default=20