bioconda.github.io - Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.
code.ohloh.net - I bet, this website will be your best friend in near future. This helps us to explore the existing open source codes and learn from it.
You can find some useful open source bioinformatics codes for your analysis work. You can use the left bar...
What are genomic interspersed repeats?
In the mid 1960's scientists discovered that many genomes contain stretches of highly repetitive DNA sequences ( see Reassociation Kinetics Experiments, and C-Value Paradox ). These sequences were later...
How to download FASTA sequence for certain gene features while in the NCBI's Sequence Viewer.
Sequence Viewer homepage:
www.ncbi.nlm.nih.gov/projects/sviewer/
Sequence Viewer playlist:
https://www.youtube.com/playlist?list=PL76D7EE6A6A8AC1C3
nematodes.org - Blobsplorer is a tool for interactive visualization of assembled DNA sequence data ("contigs") derived from (often unintentionally) mixed-species pools. It allows the simultaneous display of GC content, coverage, and taxonomic annotation for...
github.com - This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this...
github.com - medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods...
A core element in the downstream analysis for RNA-seq data involves the translation of assembled sequences into their corresponding amino acid sequences, and on the nucleotide level into the protein coding sequences (CDS) not containing any...
www.ncbi.nlm.nih.gov - Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank....
kallisto
Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets)
Software (C++)
https://pachterlab.github.io/kallisto/
Sailfish
Estimation of isoform abundances...