Results for "reads"
Bio-Scripts
Pack a perl program with their dependencies on Ubuntu !
...at https://bioinformaticsonline.com/snippets/view/41440/perl-script-to-reads-and-extract-webpage-contents...is released... Evaluation of genome assembly software based on long readsBy BioStar 409 days ago...1505 days ago
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICARD_HOME/pica...1331 days ago
- ...d with arguments: -phred33 SRR5322499_1.fastq out.trimmed.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 Automatically using 1 threads Input Reads: 72875 Surviving: 72865 (99.9...
1210 days ago
- Use pen and paper the assemble it. If you are brave enough, you can try to assemble this set of reads: CAGATGTCCT GACCTTTTCT TAAGATCTTT TCTTTAGCCG TTTCTTCTTT GAG...
1209 days ago
Download minikraken database !
...distrib minikraken2_v2_8GB_201904_UPDATE/database200mers.kmer_distrib minikraken2_v2_8GB_201904_UPDATE/hash.k2d #Check for pe reads #kraken2 --use-names --threads 4 --db minikraken2_v2_8GB_201...1208 days ago
- #Long reads bedtools bamtofastq -i input.bam -fq output.fastq #For paired-end reads: samtools sort -n input.bam -o input_sorted.bam # sort reads by identifier-name (-n) bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq
990 days ago
Commandline for paired end reads simulation with BBMap !
...✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleave...ls/bbmap/current/ align2.RandomReads3 build=1 ref=mixed.fa out=rea...s3 [build=1, ref=mixed.fa, out=reads_BBMAP250.fq, paired, interlea...paired=true read length=250 reads=100000 insert size=400-600...984 days ago
Tadpole is 250x faster than SPADes assembler !
...ect Extending contigs with reads could be done like this: t...correction or extension. reads=-1 Only process th...r the primary kmer counts. threads=X Spawn X hashing t...ck=t Undo changes to reads that have lower coverage for...970 days ago
Trim the reads in loop using Trimmomatic !
for infile in *_1.fastq.gz do base=$(basename ${infile} _1.fastq.gz) trimmomatic PE ${infile} ${base}_2.fastq.gz \ ${base}_1.trim.fastq.gz ${...949 days ago
- # make reference for randomreads.sh # randomreads.sh part of BBTools/BBMap http...io=t pbmin=0.13 pbmax=0.17 \ reads=100 paired=f \ gaussianlengt...2=illumina2.fastq.gz > random_reads_illumina.log 2>&1 #...q \ > kmergenie-illumina-raw-reads.log 2>&1 rm ../illumina.int....
922 days ago
