MEGAHIT MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly. Usage Basic usage 1 2 3 4 megahit -1 pe_1.fq -2 pe_2.fq -o out # 1 paired-end library megahit --12 interleaved.fq -o out # one paired & interleaved paired-end library megahit -1 a1.fq,b1.fq,c1.fq -2 a2.fq,b2.fq,c2.fq -r se1.fq,se2.fq -o out # 3 paired-end libraries + 2 SE libraries megahit_core contig2fastg 119 out/intermediate_contigs/k119.

Infernal - INFERence of RNA ALignment Infernal is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

HMMER: biosequence analysis using profile hidden Markov models HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). HMMER is often used together with a profile database, such as Pfam or many of the databases that participate in Interpro. But HMMER can also work with query sequences, not just profiles, just like BLAST.

tRNAscan-SE: An improved tool for transfer RNA detection tRNAscan-SE was written in the PERL (version 5) script language. Input consists of DNA or RNA sequences in FASTA format. tRNA predictions are output in standard tabular or ACeDB format. tRNAscan-SE does no tRNA detection itself, but instead combines the strengths of three independent tRNA prediction programs by negotiating the flow of information between them, performing a limited amount of post-processing, and outputting the results in one of several formats.

Hapo-G - Haplotype-Aware Polishing of Genomes Hapo-G (pronounced like apogee) is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. Activating the conda environment 1 2 bash source /local/cluster/hapog/activate.sh Add the above source command to your shell scripts to use this program in SGE submissions. Location: 1 2 $ which hapog.py /local/cluster/hapog/bin/hapog.py help message: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 $ hapog.

BLAST - Basic Local Alignment Search Tool BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. Update notes BLAST+ 2.13.0 is here! Thu, 17 Mar 2022 12:00:00 EST Starting with this release, we are including the blastn_vdb and tblastn_vdb executables in the BLAST+ distribution. These executables can directly search SRA and WGS projects without the need to build a BLAST database.