##### standard code i did for samB samples
while writing in black shell
/share/rwmwork/khanalsa ls -l
cd l.salignaData
1.Open terminal 
2.cd /share/rwmwork/khanalsa/
3. cd/lsaligna.Data
3./share/rwmwork/khanalsa$ ls -
4.mkdir lsaligna.Data
5./share/rwmwork/khanalsa$ wget https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/x48ff2erkrhtfci/PB945_SamB_Lettuce_CoreHiFi_Revio_cell1/

after this i created a soft link /symbolic link with ln -s /share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_07_04_Lettuce_HiFi 2023_07_06_HiFi
type enter
then cd 2023_07_06_HiFi
ls -l

###### **Run Hifiasm on nitro**- Sample B

nice -n 16 /share/rwmwork/fletcher/BarberaPrograms/Hifiasm/v0.18/hifiasm/hifiasm -t 250 -o SamBG /share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_07_04_Lettuce_HiFi/PB945_SamB_Lettuce_CoreHiFi_Revio_cell1/FASTA/m84066_230701_214005_s3.hifi_reads.default.fasta /share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_07_04_Lettuce_HiFi/PB927_04_SamBG_Lettuce_Revio_cell1/FASTA/m84066_230701_210859_s2.hifi_reads.default.fasta &> Hifiasm.log
######Description of codes
nice - Sets priority level to 16 (scale of 1 to 20)
-t - number of threads. Nitro has 256. Espresso has 64, Frappe has 48
-o Output prefix
Two read files to assemble
&> Save log in this file (Hifiasm.log

##### HiFism for samB
Aims start working with HiFi data:
Change directory
cd /share/rwmwork/khanalsa
2. Make a new directory
3. Change into that directory
4. Set up a new screen
screen -S Jellyfish
5. Load the software
module load jellyfish
6. run jellyfish
nice -n 5 jellyfish count -m 31 -t 32 -C -s 10G -o SamBG.2FC.jf31 <(cat /share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_07_04_Lettuce_HiFi/PB945_SamB_Lettuce_CoreHiFi_Revio_cell1/FASTA/m84066_230701_214005_s3.hifi_reads.default.fasta /share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_07_04_Lettuce_HiFi/PB927_04_SamBG_Lettuce_Revio_cell1/FASTA/m84066_230701_210859_s2.hifi_reads.default.fasta)

###### After completion of hifiasm
#Script to conver GFA to FASTA
awk '$1 == "S" {print ">"$2"\n"$3}' [GFA] > [FA]
#Load BBMAP
module load bbmap
stats.sh [FA]

you will find the data and links also
# you can use scp command examples-
scp [e-mail]:/share/rwmwork/khanalsa/2023hifiassembly/01hifiasmv0.18/intervalblast/Consensus_Interval2_50kb.png .

----------------------------------------------------------------------------

-------------------------------------------------------------------------------------------------
###### Step-1
### copy SamA samples to your pathway-oct6 friday
scp [e-mail]:/share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_09_27_Lettuce_HiFi/PB1005_Sama_Lettuce_HiFiv3_Revio_cell1/FASTA/m84066_230927_205020_s4.hifi_reads.default.fasta /share/rwmwork/khanalsa/2023hifiassembly/samA

------------------------------------------------
------------------------------------------------
###### **Please look this code for sample A**

###### Hifiasm For samA **
cd /share/rwmwork/khanalsa
2. Make a new directory (2023Hifiassembly2)
3. Change into that directory
4. Set up a new screen
(screen -S Jellyfish2)
5. Load the software
module load jellyfish
6. run jellyfish

While running your pathway should be like this
/share/rwmwork/khanalsa/2023hifiassembly2/00jellyfish
run this code then-

nice -n 5 jellyfish count -m 31 -t 32 -C -s 10G -o SamAG.2FC.jf31 <(cat /share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_09_27_Lettuce_HiFi/PB1005_Sama_Lettuce_HiFiv3_Revio_cell1/FASTA/m84066_230927_205020_s4.hifi_reads.default.fasta) share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_09_27_Lettuce_HiFi/PB1005_Sama_Lettuce_HiFiv3_Revio_cell1/FASTA/m84066_230927_205020_s4.hifi_reads.default.fasta)

or [e-mail]:/share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_09_27_Lettuce_HiFi/PB1005_Sama_Lettuce_HiFiv3_Revio_cell1/FASTA/m84066_230927_205020_s4.hifi_reads.default.fasta

(you can use only one fasta file; no problem)
#### Manual for Jellyfish
chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://genome.umd.edu/docs/JellyfishUserGuide.pdf

##### Detail explanation of codes
Navigate to the directory /share/rwmwork/khanalsa:

cd /share/rwmwork/khanalsa
This command changes your current working directory to /share/rwmwork/khanalsa.
Create a new directory named 2023Hifiassembly2:

mkdir 2023Hifiassembly2
This command creates a new directory called 2023Hifiassembly2 in the current working directory.
Change into the newly created directory:
cd 2023Hifiassembly2
This command changes your current working directory to the newly created directory, 2023Hifiassembly2.
Start a new screen session named "Jellyfish2":
screen -S Jellyfish2
This command opens a new terminal session using the screen utility with the session name "Jellyfish2". Screen allows you to run commands in a detached terminal session.
Load the Jellyfish software module:

module load jellyfish
This command loads the Jellyfish software module, making the jellyfish command available for use.
Run Jellyfish with the following parameters:

nice -n 5 jellyfish count -m 31 -t 32 -C -s 10G -o SamaG.2FC.jf31 <(cat /share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_09_27_Lettuce_HiFi/PB1005_Sama_Lettuce_HiFiv3_Revio_cell1/FASTA/m84066_230927_205020_s4.hifi_reads.default.fasta /share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_09_27_Lettuce_HiFi/PB1005_Sama_Lettuce_HiFiv3_Revio_cell1/FASTA/m84066_230927_205020_s4.hifi_reads.default.fasta)

This command runs the jellyfish program with the following options:
nice -n =nice is way to set prority in cluster (nice ranges from 1-20)
-m 31: Sets the size of k-mers to 31.(kmer is basically length string and it simplifies the DNA sequence)
-t 32: Specifies the number of threads to use (32 in this case).
-C: Indicates that the input sequences are in canonical form (forward strand only); look both strands??
-s 10G: Sets the memory limit to 10 gigabytes.
-o SamaG.2FC.jf31: Specifies the output file as SamaG.2FC.jf31.
<(...): This is process substitution in Bash. It takes the concatenated contents of two input files (specified in the parentheses) and uses them as input to the jellyfish count command.

---------------------------------------------------

###### my full path /share/rwmwork/khanalsa/2023hifiassembly/samA

For sample samA
###### After completion of jellyfish running
jellyfish histo SamAG.2FC.jf31 > SamAG.2FC.jf31.txt

-Use scp command to get the files into local computer
-Load to genomoscope
-Get the picture

#### ######## **Run Hifiasm on nitro**- Sample A

nice -n 16 /share/rwmwork/fletcher/BarberaPrograms/Hifiasm/v0.18/hifiasm/hifiasm -t 250 -o SamAG
/share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_09_27_Lettuce_HiFi/PB1005_Sama_Lettuce_HiFiv3_Revio_cell1/FASTA/m84066_230927_205020_s4.hifi_reads.default.fasta
/share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_09_27_Lettuce_HiFi/PB1005_Sama_Lettuce_HiFiv3_Revio_cell1/FASTA/m84066_230927_205020_s4.hifi_reads.default.fasta &> Hifiasm.log

### nice - Sets priority level to 16 (scale of 1 to 20)
-t - number of threads. Nitro has 256. Espresso has 64, Frappe has 48
-o Output prefix
Two read files to assemble
&> Save log in this file (Hifiasm.log) (edited)

##### After completion of hifiasm get ready for statistics
###### After completion of hifiasm
#Script to conver GFA to FASTA
awk '$1 == "S" {print ">"$2"\n"$3}' [GFA] > [FA]
#Load BBMAP
module load bbmap
stats.sh [FA]

###### **Steps**
###### Details of codes used

nice -n 16: This part of the command runs the nice utility, which allows you to set the priority of the command. A higher priority value (lower nice value) means the command will use fewer system resources. In this case, the priority is set to 16. This value is used to control the CPU scheduling priority of the subsequent command.

/share/rwmwork/fletcher/BarberaPrograms/Hifiasm/v0.18/hifiasm/hifiasm: This is the path to the Hifiasm executable. Hifiasm is a genome assembler.

-t 250: This option specifies the number of threads or CPU cores to be used for the assembly process. In this case, it's set to 250 threads, which means the assembly will be highly parallelized and will make use of multiple CPU cores.

-o SamAG: This option specifies the output prefix for the assembly results. The assembled genome will be saved with this prefix.

/share/rwmstore/Reads_DNA_RWM/PacBio/Lettuce/2023_09_27_Lettuce_HiFi/PB1005_Sama_Lettuce_HiFiv3_Revio_cell1/FASTA/m84066_230927_205020_s4.hifi_reads.default.fasta: These are the input FASTA files containing PacBio HiFi reads for Sample A. It appears that the same file is specified twice as input.
&> Hifiasm.log: This part of the command redirects both standard output (stdout) and standard error (stderr) to a log file named Hifiasm.log. This log file will capture any messages or errors generated during the Hifiasm assembly process.

###### After getting haplo1 and haplo2 assembly, we can go for mummer plot, blastn, mapping and other further process.

###### note
Please keep calm: one day will come for you!When everyone will support you: you are not alone;your mom is there :) :)