Results for "454 data"
Bio-Scripts
Install grabseqs using conda !
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1106 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS=...me.aligned.bam bcftools mpileup -O b -o results/bcf/$basename.bcf -f data/ref_genome/sequences.fasta re...1096 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/M...Primary input file for reads to use as kmer data. in2= Second input file for paired data. extra= Extra files f...stantially better assemblies for low-depth data, but they are very slow for l...1028 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15I...vironment.yml Collecting package metadata (repodata.json): done Solving environm...############## | 100% importlib-metadata-4 | 32 KB | #############...need to manually update the taxonomy databases before Krona can generat...975 days ago
Run Pango on your multifasta file !
#More at https://cov-lineages.org/resource.... The query file is:/home/jnarayan/RF_DATA/FASTA/Input_for_Cova_all_samp...etected: 320 Total passing QC: 293 Data files found: Trained model:...put file written to: /home/jnarayan/RF_DATA/FASTA/lineage_report.csv (pa...939 days ago
Installing SEVA environment in Conda !
(base) [jnarayan@hn1 SEVA_codes_and_files]$ conda env create -f SEVA.yaml Collecting package metadata (repodata.json): done Solving environm...####################################### | 100% r-data.table-1.14.0 | 2.0 MB | #...889 days ago
Install StringTie on ubuntu / Linux !
#StringTie is a software program to perform transcript assembly and quantification of RNAseq data. The binary distributions are...875 days ago
Install Varscan on Ubuntu / Linux !
#Varscan is a java program designed to call variants in sequencing data. It was developed at the Genome Institute...875 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data470 days ago
Download lumpy skin disease data !
Location https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=880745 The raw genome sequence data from the 2022 outbreak in India is available in the SRA Project PRJNA880745462 days ago
