SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, se...1984 days ago
NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
NxRepair is a python module that automatically detects large...f an identified misassembly and will generate a new fasta file containing both the corr...nxrepair aligned_matepairs.bam assemblyfasta.fasta error_locations.csv new...1980 days ago
GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research
GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multi...1978 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codon...ying algorithm see the original publication:MACSE: Multi...1955 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a us...1869 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
...sciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Geno...iences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR dupli...1798 days ago
MSAProbs - Parallel and accurate multiple sequence alignment
MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden M...1814 days ago
Cactus: a reference-free whole-genome multiple alignment program
Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111 Cactus uses sub...1780 days ago
1761 days ago
Kalign: fast multiple sequence alignment program for biological sequences.
Kalign is a fast multiple sequence alignment program for biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf...1700 days ago