seqtk
foldseek
seqtk | foldseek | |
---|---|---|
8 | 1 | |
1,314 | 642 | |
- | 6.7% | |
5.1 | 9.3 | |
7 months ago | 6 days ago | |
C | C | |
MIT License | GNU General Public License v3.0 only |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
seqtk
-
Illumina adapters and quality trimming
seqtk: A lightweight and versatile tool for processing FASTQ and FASTA files. https://github.com/lh3/seqtk
-
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
-
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
-
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.
-
Reverse sequencing of fastq file
It's a little toolkit written by one of the Illuminati of the Bioinformatics world: seqtk on GH
-
[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?
-
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.
foldseek
-
AI predicts shape of nearly every known protein
"Some sophisticated applications of the expanded AlphaFold database might also depend on downloading its entire 23 terabyte contents, which won’t be feasible for many teams, Steinegger says. Cloud-based storage could also prove costly. Steinegger has co-developed a software tool called FoldSeek that can quickly find structurally similar proteins and which should be able to squash the AlphaFold data down considerably."
[FoldSeek Search](https://search.foldseek.com/search)
[Github:FoldSeek](https://github.com/steineggerlab/foldseek)
What are some alternatives?
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
samtools - [Moved to: https://github.com/ingolia/SamTools]
DAGSfM - Distributed and Graph-based Structure from Motion. This project includes the official implementation of our Pattern Recognition 2020 paper: Graph-Based Parallel Large Scale Structure from Motion.
htslib - C library for high-throughput sequencing data formats
hh-suite - Remote protein homology detection suite.
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
MooseFS - MooseFS – Open Source, Petabyte, Fault-Tolerant, Highly Performing, Scalable Network Distributed File System (Software-Defined Storage)
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
mars - Asynchronous Block-Level Storage Replication
bam-filter - Use simple expressions to filter a BAM/CRAM file
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite