Results for "Fastq"
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...3770 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...3619 days ago
- ...linux command from within python code Example: if you want to run fastqc for QC of fastq file: from subprocess import...,"fastq","-o", "/home/name/result/","/dev/stdin"],stdin=fopen("read.fastq","r") ,stdout=PIPE,stderr=PIP...
3540 days ago
- ...formats. It supports, and can inter-convert: fastq fasta fasta+qual sam scarf (a...e to follow naming conventions, or out-of-spec fastq files with qualities values l...invocation. Typical usage examples: Reformat fastq into fasta: reformat.sh in=x....
2705 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...k interface Takes NGS data (.fastq, BAM, SAM), microarrays (Affy...so give raw reads in Fasta or Fastq Reference Sequence used to a...BWA mapping program; Input: FASTQ, Reference sequence file and...mitocondrial variants Input:FASTQ, pileup Reference sequence:...2900 days ago
- ...gov/nuccore/NC_008253 contains entire genome for Escherichia coli 536. FASTQ Format: text format for stori...entifier of a raw sequence read (also known as the Query Name). Used in FASTQ and SAM files. paired-end se...
2860 days ago
Genome Assembly Tools and Software - PART1 !!
...d additional files van be downloaded below. The input data is given by pre-assembled scaffold sequences (FASTA) and NGS paired-read data (FASTA or FASTQ). SSAKE 3.8.4 – As...2677 days ago
- ...like this may suffice: spades.py -t 4 \ -m 32 \ -k 31,51,71 \ --only-assembler \ -1 miseq.1.fastq -2 miseq.2.fastq \ --nanopore minio...
2342 days ago
Run miniasm assembler on nanopore reads !
... unitig sequences. Thus the per-base error rate is similar to the raw input reads. Find the detail of the reads repeats: fq2fa ONT_A.fastq ONT_A.fasta minimap2 -xa...2321 days ago
- ...'1~4s/^@/>/p;2~4p' INFILE.fastq > OUTFILE.fasta Using P...using paste cat INFILE.fastq | paste - - - - |cut -f 1, 2|...gt; file.fa FASTX-toolkit fastq_to_fasta is available in...wk Another option to convert fastq to fasta format using bi...
2296 days ago
