Kmer: a suite of tools for DNA sequence analysis
...throughput batched alignment. LEAFF: LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing ran...1049 days ago
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OGDRAW - Draw Organelle Genome Maps
...at into graphical maps. The input has to be a GenBank or EMBL/ENA flat file wherase the output can vary among several types of files. The application is optimized...1000 days ago
RNA-seq workflow: gene-level exploratory analysis and differential expression
Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified...996 days ago
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SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files
...se program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to i...gram delivering high performance analyses Supports FASTA/FASTQ files, also Gzip compressed A grow...853 days ago
Quip: Aggressive compression of FASTQ, SAM and BAM files.
This will help us to reduce the amount of drive space we take up and decrease data transfer times Quip compresses next-generation sequencing data with extreme prejudi...769 days ago
ALE: Assembly Likelihood Estimator
Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.481 days ago