Dot, an interactive viewer for genome-genome comparison
...ts to visualize genome-genome alignments in order to evaluate new assemblies and perform exploratory comparative genomics. Dot supports the output of MUMmer’s nucmer alig...2302 days ago
2290 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
.... In this evaluation framework, repeats are taken into account. The new evaluation framework considers the optimal assignment of contigs in the output scaffolding to contigs in the...2236 days ago
MIX: Combining multiple assemblies from NGS data
...s of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a pat...2188 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
...functionality that it is necessary in most of the cases. Other options can be changed in the stand-alone program. You can see here an example output file showing the blocks...2163 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some qu...2161 days ago
PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
...l reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non-paired data, or contigs that were output from a prior run of PRICE or...2154 days ago
2173 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
...d reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be com...2172 days ago
WhatsHap: fast and accurate read-based phasing
...: Pass in a VCF and one or more BAM files, get out a phased VCF. Supports multi-sample VCFs. It produces standard-compliant VCF output by default If desired, get output that is compatible with ReadB...2168 days ago