Results for "QC"
Bio-Scripts
BASH script for SelfBLAST a genome
...ery $SEQ -db $MYDB -evalue 1e-5 -num_threads $THREAD -max_target_seqs 1 -outfmt '6 qseqid staxid qstart qend sseqid sstart send evalue length frames qcovs' -out $OUTFILE; echo "D...2649 days ago
- library(vcfR) # Input the files. vcf
2057 days ago
Samtools commands for bioinformatician !
...ls depth -a sorted_dupremoved.bam | awk '{c++; if($3>0) total+=1}END{print (total/c)*100}' ### flagstat # output file has two columns: QC-passed reads and QC-failed reads # and rows: tot...1600 days ago
- (JitMetaENV) ➜ JitMeta conda install -c bioconda fastqc Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.
1213 days ago
Install trimmomatic using conda !
(JitMetaENV) ➜ fastQC_out conda install -c bioconda trimmomatic Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1213 days ago
- (JitMetaENV) ➜ fastQC_out trimmomatic SE -phred33 SRR5322499_1.fastq out.trimmed.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 TrimmomaticSE: Started with arguments...
1213 days ago
- (JitMetaENV) ➜ fastQC_out conda install -c bioconda spades Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.
1213 days ago
Run Pango on your multifasta file !
...s satisfied. The query file is:/home/jnarayan/RF_DATA/FASTA/Input_for_Cova_all_samples_combined.fa ** Running sequence QC ** Number of sequences detected: 320 Total passing QC: 293 Data files found: Tr...884 days ago
Script to rapid genome clustering based on pairwise ANI
...UCLUST-like clustering using the MIUVIG recommended-parameters (95% ANI + 85% AF): aniclust.py --fna --ani --out --min_ani 95 --min_tcov 85 --min_qcov 0632 days ago
- (jitENV) [jnarayan@hn1 preetiDATA]$ blastn -task blastn -query list_flank_0.fa -subject ../monkeypoxDATA_07_06_22/JIT_gisaid_pox_2022_09_06_07.fasta -evalue 20000000 -word_size 5 -num_threads 4 -outfmt 6 -out blastn_0.txt -qcov_hsp_perc 100 -perc_identity 100 -max_target_seqs 10000
589 days ago
