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https://github.com/applicativesystem/miseq-nextseq-novaseq-assembly
quality control, genome assembly, mapping for miseq, novaseq and nextseq reads
https://github.com/applicativesystem/miseq-nextseq-novaseq-assembly
bioinformatics genome-assembly genome-sequencing illumina illumina-sequencing miseq nextseq
Last synced: 24 days ago
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quality control, genome assembly, mapping for miseq, novaseq and nextseq reads
- Host: GitHub
- URL: https://github.com/applicativesystem/miseq-nextseq-novaseq-assembly
- Owner: applicativesystem
- License: mit
- Created: 2024-08-20T18:53:41.000Z (5 months ago)
- Default Branch: main
- Last Pushed: 2024-08-20T20:00:51.000Z (5 months ago)
- Last Synced: 2024-11-10T20:18:16.787Z (about 2 months ago)
- Topics: bioinformatics, genome-assembly, genome-sequencing, illumina, illumina-sequencing, miseq, nextseq
- Language: Shell
- Homepage:
- Size: 1.95 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# miseq-nextseq-novaseq-genome
- A pure shell assembler that takes only the directory path and does all the cleaning of the reads, mapping, remapping and assembly.
- From start to finish everything by providing a simple directory path. You dont have to provide anything else just the directory path of the fastq files.
- It works with MiSeq, NextSeq, NovaSeq. It works with all plant, bacterial and fungal genomes.
```
shell_command
hi there i am a denovo assembler script which will check your fastq files, \
clean then and assemble them coming from the illumina platform. I take MiSeq, NextSeq,\
NovaSeq reads, you can just clean, or clean and map or clean and assemble.As of the \
current it supports the cleaning through the fastp, mapping through the bowtie2 and \
assembly using the spades I will add more assembler to this interface and also multiple \
assembly configurations. Currently, it supports 45, 55, 65 kmers you can change the \
kmer according to the assembly preferences.\
# if from cleaning only
main ✗ $ sh genome_cleaner.sh
enter the name of the directory: /Users/gauravsablok/Desktop/GitHub/shell_builder \
do you want to clean the reads:yes \
enter the number of the threads:1 \
do you want to map the reads:no \
enter the name of the bowtie index:no \
do you want to assemble the reads:no \
Processing the cleaning of the reads file from the sequencing runs
fastp --in1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt \
--out1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R1 \
--in2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text1 \
--out2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R2 --threads 1 \
# if cleaning to remapping files
enter the name of the directory: /Users/gauravsablok/Desktop/GitHub/shell_builder \
do you want to clean the reads:yes \
enter the number of the threads:1 \
do you want to map the reads:yes \
enter the name of the bowtie index:gaurav \
do you want to assemble the reads:no \
Processing the cleaning of the reads file from the sequencing runs \
fastp --in1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt \
--out1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R1 \
--in2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text1 \
--out2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R2 --threads 1 \
bowtie2-build gaurav gaurav \
bowtie2 -t -x gaurav -p 1 --very-sensitive-local -1 \
/Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R1 \
-2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text3.txt.cleaned.R2 \
-S gaurav.sam --no-unal --al-conc gaurav.aligned.fastq \
# if from cleaning to assembly configuration \
enter the name of the directory: /Users/gauravsablok/Desktop/GitHub/shell_builder \
do you want to clean the reads:yes \
enter the number of the threads:1 \
do you want to map the reads:yes \
enter the name of the bowtie index:gaurav \
do you want to assemble the reads:yes \
Processing the cleaning of the reads file from the sequencing runs \
fastp --in1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt \
--out1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R1 \
--in2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text1 \
--out2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R2 --threads 1 \
bowtie2-build gaurav gaurav \
bowtie2 -t -x gaurav -p 1 --very-sensitive-local -1 \
/Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R1 \
-2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text3.txt.cleaned.R2 \
-S gaurav.sam --no-unal --al-conc gaurav.aligned.fastq \
spades.py -1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.aligned.R1.fastq \
-2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.aligned.R2.fastq \
--careful --threads 1 --tmp-dir -k 45,55,65,75 \
-o /Users/gauravsablok/Desktop/GitHub/shell_builder/ \
```
Gaurav Sablok \
University of Potsdam \
Potsdam,Germany