Results for "short reads mapping"
Bio-Scripts
Commandline for paired end reads simulation with BBMap !
(JitMetaENV) ➜ mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleave...s/bbmap/current/ align2.RandomReads3 build=1 ref=mixed.fa out=rea...3 [build=1, ref=mixed.fa, out=reads_BBMAP250.fq, paired, interlea...paired=true read length=250 reads=1...1004 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpol...correction or extension. reads=-1 Only process th...r the primary kmer counts. threads=X Spawn X hashing t...(minc) Do not write contigs shorter than this. mincoverage=1...ck=t Undo changes to reads t...990 days ago
Trim the reads in loop using Trimmomatic !
for infile in *_1.fastq.gz do base=$(basename ${infile} _1.fastq.gz) trimmomatic PE ${infile} ${base}_2.fastq.gz \ ${base}_1.trim.fastq.gz ${b...968 days ago
- # make reference for randomreads.sh # randomreads.sh part of BBTools/BBMap http...tics/elbers/bbmap-38.86/randomreads.sh build=1 \ seed=1 \ ref=G...io=t pbmin=0.13 pbmax=0.17 \ reads=100 paired=f \ gaussianlengt...2=illumina2.fastq.gz > random_reads_illumina.log 2>&1 #...
942 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp123/hifiasm/issues/33 # Use Drosophila melon...pe0.fasta.gz # make reference for randomreads.sh # randomreads.sh part of BBTools/BBMap http...max 12000bp /genetics/elbers/bbmap-38.86/randomreads.s...931 days ago
- bowtie2-build toy_dataset_contig_for_mapping.fasta toy_dataset_contig_for_mapping.btindex bowtie2 -x toy_dataset_contig_for_mapping.btindex -f -U toy_dataset_reads_for_mapping.fasta -S toy_dataset_mapped_species1.sam samtools sort toy_dataset_...
881 days ago
BBmap the reads with all alignments !
bbmap.sh in=../reference/reference.numbered.fa ambig=all vslow perfectmode maxsites=100000 out=fetch_Ids_for_barcode.sam832 days ago
Bash command to count reads in fastq file !
#ref fastq file #ref1_1.fq) echo $(( $(wc -l805 days ago
Awk command to keep only short the fasta header !
awk '/^>/ {$0=$1} 1' file.fasta723 days ago
- (jitENV) [jnarayan@hn1 preetiDATA]$ 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
606 days ago
