github.com - Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs...
github.com - PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
More at https://github.com/neufeld/pandaseq
github.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....
github.com - Gepard (German: "cheetah", Backronym for "GEnome PAir - Rapid Dotter") allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes. Reference: Krumsiek J, Arnold R, Rattei T. Gepard: A rapid and sensitive tool...
github.com - PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to identify the most likely prophage regions.
Initial versions of PhiSpy were written by
Sajia Akhter...
github.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...
mira-assembler.sourceforge.net - MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assembles/maps reads gained by
electrophoresis sequencing (aka Sanger sequencing)
454 pyro-sequencing (GS20, FLX or Titanium)
Ion...
www.atgc-montpellier.fr - LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read...