2310 days ago
Alfred: BAM Statistics and Feature Counting
The easiest way to get Alfred is to download a statically linked binary from the Alfred github release page. Alternatively, you can build Alfred from source. Alfr...2307 days ago
Circoletto: visualizing sequence similarity with Circos
...pleasing and informative overview of sequence similarity search results. Online version and downloadable software package for offline use (source code in PERL) freely available at&...2290 days ago
Generate interactive codon usage plots
Generate interactive codon usage plots as used at ensembl.lepbase.org. The input file format can be generated from an Ensembl database using the export_json.pl script from the easy-import pipeline. live demo2271 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
...s, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), and synteny). One is comparing human GENCODE genes (from GENCODE v30) to lncRNAs from other sp...862 days ago
Carefully opt for human reference genome
Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 huma...1551 days ago
2234 days ago
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Usin...2222 days ago
2221 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
...n the pipeline can be found here. we recommend Trinity for the assembly. Trinity components should be merged with cap3. Our code to perform the merging is ava...2179 days ago