seqtk
samtools
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seqtk
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Illumina adapters and quality trimming
seqtk: A lightweight and versatile tool for processing FASTQ and FASTA files. https://github.com/lh3/seqtk
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looking for a tool to filter non-coding regions/excise ORFs from a draft assembly
Perhaps seqtk could be helpful https://github.com/lh3/seqtk
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Help with understanding awk code
You could also check out tools specialized for FASTA processing like https://github.com/shenwei356/seqkit and https://github.com/lh3/seqtk
- !help
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Doubts with my first ever mRNA-seq QC analysis
If I were to analyze I would use a random fastq sampler like Seqtk and bring all your samples to a lowest read depth of your 27 libraries although I wouldn't analyze a library with less than 2mil reads. 5 mil is fine for differential, you can obviously get more reads and probably received more information but increasing read depth may plateau.
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Reverse sequencing of fastq file
It's a little toolkit written by one of the Illuminati of the Bioinformatics world: seqtk on GH
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[Help] Copying head of fastq file into a .txt file named .fastq, doesn't include the header resolving in an error when converting to .bam file.
I recommend installing seqtk, which makes this easy. Of course sed/awk/perl are theoretically entirely sufficient but why make life more difficult than necessary?
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Looking for small SRA Data Sets
Most SRA files are grouped by projects. On a basic level for something common like RNA-seq you will have replicates of the control and treatment/diseased samples. Each file (i.e. sample) contains raw sequencing reads, usually millions per sample. You could randomly subsample the sequencing reads very easily using many tools (common choice is https://github.com/lh3/seqtk). There is no way you are going to assemble an animal genome with MB file sizes (for example the human genome itself is already over 3GB in size). You should probably look for bacterial or viral DNA samples and subset those to an appropriate size.
samtools
We haven't tracked posts mentioning samtools yet.
Tracking mentions began in Dec 2020.
What are some alternatives?
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Genbank - Genbank format tools and parser
htslib - C library for high-throughput sequencing data formats
ViennaRNAParser
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
libdna - ♥ Essential Functions for DNA Manipulation
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
RNAlien - RNAlien - unsupervised RNA family model construction
bam-filter - Use simple expressions to filter a BAM/CRAM file
phybin - Binning (Newick) Phylogenetic Trees by Topology
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
BlastHTTP - Haskell cabal libary for submission and result retrieval from the NCBI Blast REST webservice