Results for "split reads"
Top-level pages
BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries
BBSplit internally uses BBMap to map reads to multiple genomes at once,...uo; flag. The normal use of BBSplit is like Seal, either quantifying how many reads go to each reference, or spli...lmonella, you could do this:bbsplit.sh in=reads.fq ref=ecoli.fa,s...2315 days ago
- There are several ways you can convert fastq to fasta sequences. S...or many purposes. One such use is fastq-fasta conversion seqret -sequence reads.fastq -outseq reads.fasta awk can be used...
2306 days ago
PerlOneLiner for Bioinformatician
FILE SPACING------------ # Double space a fileperl -pe '$\="\n"'perl -pe 'BEGIN { $\="..."@list"' # Create an array from a string@months = split ' ', "Jan Feb Mar Apr May Jun...in the stringperl -le 'print join ", ", map { ord } split...2302 days ago
List of visualization tools for genome alignments
Genome browsers are useful not only for showing fina...or.htm JVM Java Visual Mapping tool for NGS reads http://www.springer.com/cda/...gnments of huge-scale single-end and pair-end short reads http://omictools.com/mapview...2284 days ago
Awk for Bioinformatician and computational biologist
...ions} /pattern2/ {Actions}' file The working of Awk is as followsAwk reads the input files one line at a...TATATAAwk has number of builtin variables. For each record i.e line, it splits the record delimited by whit...2280 days ago
Some useful Bioinformatics links
...apping of nanopore sequencing reads with GraphMap | Nature Commun...s/ncomms11307 lumpy-sv/extractSplitReads_BwaMem at master ·...sv/blob/master/scripts/extractSplitReads_BwaMem jts/nanocorrect:...ols.html How To Filter Mapped Reads With Samtools https://www.bi...2242 days ago
- ...ete_dataset/"$line"; done To split bam files into sets with mapped and unmapped reads: samtools view -F4 sample.ba...-f1 < your_file To count reads in a all .fastq.gz files in y...ead length distribution: cat reads.fastq | awk '{if(NR%4==2) pri...
2218 days ago
Gap filling or Contigs extensions tools !
There are many tools to perform gap...to fill the gap within paired reads" or "Toward almost closed gen...local re-assemblies using 454 reads. We used GAPresolution but it...of interest, and the set S of reads those contigs contain. Let C...ctor, and generate paired-end reads for this library; then try st...2165 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ &&am...2182 days ago
LINKS scaffolder bloomfilter setting !
➜ bin git:(master) ✗ ls -l total 68 drwxrwxr-x 3 urbe...-s file-of-filenames, full path to long sequence reads or MPET pairs [see below] (Multi-FASTA/fastq format, required) -m MPET reads (default -m 1 = yes, default...2151 days ago
