GFinisher: a new strategy to refine and finish bacterial genome assemblies
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaf...2103 days ago
Indexcov: fast coverage quality control for whole-genome sequencing
indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize po...2069 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
...nd evolution Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved...2074 days ago
Ensembl Variation - Calculated variant consequences
For each variant that is mapped to the reference genome, we identify all overlapping Ensembl transcripts. We then use a rule-based approach to predict the effects that each allele of t...2058 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
...ontig and an associated haplotig. This can be an issue for downstream analysis whether you're working on the haploid or phased-diploid assembly. Identify pairs of contigs that are syn...1959 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
...daries are subject to re-adjustment using supporting information of TG..CA box and TSRs and reliable LTRs are selected. Next, LTR_FINDER tries to identify PBS, PPT and RT inside LTR pa...1932 days ago
SvABA: Genome-wide detection of structural variants and indels by local assembly
...eads at the command line using VariantBam rules. These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants. Sequencing reads ar...1924 days ago
gEVAL: Genome Evaluation Browser
...enome assemblies through its tools and pre-computed analyses. The strength of this browser is the ability to navigate an up to date assembly and identify problematic regions and assis...1776 days ago
GEO2R: compare two or more groups of Samples
GEO2R to compare two or more groups of Samples in order to identify genes that are differentially expressed across experimental conditions.1225 days ago
StringTie Transcript assembly and quantification for RNA-Seq
...t can also be used by other transcript assemblers, but also alignments of longer sequences that have been assembled from those reads. In order to identify differentially expressed gene...1419 days ago