Results for "fastq"
Blogs
BBTools for bioinformatician !
...h means N (in either fasta or fastq format). The BBMap package au...mat.sh in=reads.sam out=reads.fastq Verify pairing and optio...0 adderrors=false out=perfect.fastq reads=1000 minlength=18 maxle...omma-delimited (e.g. in=file1.fastq,file2.fastq,file3.fastq). And...2271 days ago
- ...have paired reads and # you expect high gene density with UTR # overlap (use FASTQ input file format #...
2133 days ago
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Bookmarks
- ...s using Locally ConsistentEncoding) is a tool for compressing FASTQ files. It is designed specifically for the Illumina-generated FASTQ files, but supports any valid...
2942 days ago
- FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly...
1273 days ago
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Files
- ...n_core] convert to sequence coordinate... 1.00 sec[bwa_aln_core] refine gapped alignments... 6.07 sec[bwa_aln_core] print alignments... PREPROCESS:Fastq format is recognized[Thu Jun...
2152 days ago
Pages
Genome Assembly Tools and Software - PART2 !!
...alability in mind. It can assemble large and high-coverage genomes from fastq files in a short time and pro...e-assembled contig sequences (FASTA) and NGS paired-read data (FASTA or FASTQ). The final scaffolds are pro...2686 days ago
Top-level pages
Useful Publications and Websites for Deep Sequencing Data Analysis
...Res 21(5):734-40, 2011. Full Text Compression of DNA sequence reads in FASTQ format. Deorowicz & Grabo...equencing errors. Kelley et al, Genome Biol 11(11):R116, 2010. PubMed FastQC: a quality control tool for...3780 days ago
Perl one-liner for bioinformatician !!!
...encing data most of the bioinformaticians mung and wrangle around massive amounts of genomics text. There are several "standardized" file formats (FASTQ, SAM, VCF, etc.) and some too...3628 days ago
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Wire posts
Bio-Scripts
Extract the fastq sequence with range in Perl
use Bio::DB::Fasta; open(POSITIONS,"positions.txt"); while(){ chomp; my ($seqName,$begin,$end) = split(/\s/); my $db = Bio::DB::Fasta->new('allGenomeContacted.fa'); my $seq = $db->seq("$seqName", $begin => $end); print "$seq\n"; } close(POSITIONS);2468 days ago
Convert fastq to fasta in Perl
use Bio::SeqIO; #convert .fastq.gz to .fasta open my $zcat, 'zcat seq.fastq.gz |' or die $!; my $in=Bio::SeqIO->new(-fh=>$zcat, -format=>'fastq'); my $out=Bio::SeqIO->new(-...2331 days ago
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Tags
- There are several ways you can convert fastq to fasta sequences. Some methods are listed below. Using SED sed can be used to selectively print the desired lines from a file, so if you print the first and 2rd line of every 4 lines, you get the sequence header and sequence need...
Tags: fasta, fastq, convert, sed, awk, seqtk, bioawk, fastx, Emboss, fastq2fasta
2305 days ago
Comments
Comment on "A quick guide to Phred scaling"
...quality scores are typically encoded in the quality score field of the FASTQ file format, which is a commo...h base call and are typically encoded in the quality score field of the FASTQ file format....416 days ago
Comment on "Short-read assembly using Spades !"
.... This step can be performed using various tools such as Trimmomatic or FastQC. Running SPAdes: After...is usually as follows: spades.py -o output_directory -1 forward_reads.fastq -2 reverse_reads.fastq Here,...416 days ago
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