Results for "long reads"
Bio-Scripts
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ sudo apt...bstdc++-7-dev libsys-hostname-long-perl libtcl8.6 libtinfo-dev l...bstdc++-7-dev libsys-hostname-long-perl libtcl8.6 libtinfo-dev l...ic/main amd64 libsys-hostname-long-perl all 1.5-1 [11.7 kB]...ected package libsys-hostname-long-...1066 days ago
- #Long reads bedtools bamtofastq -i input.bam -fq output.fastq #For paired-end reads: samtools sort -n input.bam -o input_sorted.bam # sort reads by identifier-name (-n) bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq
1008 days ago
Commandline for paired end reads simulation with BBMap !
.../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=100000 insert size=400-600...1002 days ago
Tadpole is 250x faster than SPADes assembler !
...r the primary kmer counts. threads=X Spawn X hashing t...xtend: Extend sequences to be longer, and optionally...ck=t Undo changes to reads that have lower coverage for...) Discard shavings up to this long. Note: Shave and rinse can pr...988 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 ${...967 days ago
- # make reference for randomreads.sh # randomreads.sh part of BBTools/BBMap h...io=t pbmin=0.13 pbmax=0.17 \ reads=100 paired=f \ gaussianlengt...a of k-mer with that produces longest N50 # http://kmergenie.bx....q \ > kmergenie-illumina-raw-reads.log 2>&1 rm ../illumina.int....
940 days ago
Bash script to simulate a genome !
...issues/33 # Use Drosophila melongaster PacBio assembly cd /gen...# make reference for randomreads.sh # randomreads.sh part of BBTools/BBMap http...dea of k-mer with that produces longest N50 # http://kmergenie.bx....netics/elbers/bbmap-38.86/randomreads.sh build=1 \ ow=t seed=1 \...929 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.sam830 days ago
Bash command to count reads in fastq file !
#ref fastq file #ref1_1.fq) echo $(( $(wc -l803 days ago
Extract the mapped and unmapped reads !
PROCESSORS=20 #Single_End_Layout: samtools view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam samtools view --threads $PROCESSORS -b -f 4 in.bam >...m #Paired_End_Layout samtools view --threads $PROCESSORS -b -f 2 in.bam >...602 days ago
