Comments (5)
Running code:
#Set input and parameters
round=2
threads=20
read1=../00.raw_data/SRR12578435_R1.fastq
read2=../00.raw_data/SRR12578435_R2.fastq
input=../01.nextDenovo/01_rundir/03.ctg_graph/nd.asm.fasta
for ((i=1; i<=${round};i++)); do
#step 1:
#index the genome file and do alignment
bwa index ${input};
bwa mem -t ${threads} ${input} ${read1} ${read2}|samtools view --threads 3 -F 0x4 -b -|samtools fixmate -m --threads 3 - -|samtools sort -m 2g --threads 5 -|samtools markdup --threads 5 -r - sgs.sort.bam
#index bam and genome files
samtools index -@ ${threads} sgs.sort.bam;
samtools faidx ${input};
#polish genome file
/data/chaofan/software/NextPolish/lib/nextpolish1.py -g ${input} -t 1 -p ${threads} -s sgs.sort.bam > genome.polishtemp.fa;
input=genome.polishtemp.fa;
#step2:
#index genome file and do alignment
bwa index ${input};
bwa mem -t ${threads} ${input} ${read1} ${read2}|samtools view --threads 3 -F 0x4 -b -|samtools fixmate -m --threads 3 - -|samtools sort -m 2g --threads 5 -|samtools markdup --threads 5 -r - sgs.sort.bam
#index bam and genome files
samtools index -@ ${threads} sgs.sort.bam;
samtools faidx ${input};
#polish genome file
/data/chaofan/software/NextPolish/lib/nextpolish1.py -g ${input} -t 2 -p ${threads} -s sgs.sort.bam > genome.nextpolish.fa;
input=genome.nextpolish.fa;
done;
#Finally polished genome file: genome.nextpolish.fa
from nextpolish.
Thank you for your reply!
from nextpolish.
Check the maping quality and wether these alignments are primary alignments?
from nextpolish.
Repeat region1
Repeat region2
Hi! @moold. Sorry for my late reply. There are many breakpoints (for Illumina reads) in this region.
I don‘t know how to check the primary alignments
.
from nextpolish.
Nextpolish use the 0xC04
flag to filter alignments, so you I think these alignments should have these flags。
from nextpolish.
Related Issues (20)
- Empty bin directory after installation? HOT 2
- User defined alignment pipeline for short- and long-reads HOT 2
- [question] combine with medaka or not? HOT 3
- run nextplolish2.py sleep HOT 8
- Ignore the secondary alignment HOT 2
- Test run failed at map_genome: "[gzclose] buffer error" HOT 3
- Installation failure with multiple definition of 'rle_auxtab' HOT 2
- db_split failed: HOT 3
- How does NextPolish polish an assembly with long reads? HOT 1
- make[2]: *** [Makefile:30: bwa] Error 1 错误 HOT 1
- slurmstepd: error: JOB CANCELLED DUE TO TIME LIMIT HOT 1
- run fails with long read only in conda env HOT 5
- SLURM out of memory and time... HOT 1
- [main_samview] fail to read the header from "-" HOT 1
- zlib.h not found error HOT 1
- polish_genome failed HOT 1
- problem with NextPolish-CentOS6.9.tgz
- The process of polishing causes a significant decrease in genome size. HOT 8
- During the execution of samtools index, I encountered an error: "invalid option -- '@'" HOT 4
- An error message was encountered while running 00.lgs_polish/04.polish.ref.sh.work/polish_genome01
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from nextpolish.